You can use the optional argument for the section (inside [...]) which will used for running content:
\documentclass{article}
\usepackage{lipsum}
\begin{document}
\tableofcontents
\section[my section]{This is going to \\ go for two lines}
\lipsum
\end{document}
Make sure to use a short title in the optional argument.
the blank page after your bold paragraph is simply because you forced a pagebreak with \onecolumn. I'm not sure quite the layout you want but you want to avoid forced breaks and use the * form to allow page wide floats, something like
\documentclass[twocolumn]{article}
\usepackage[utf8]{inputenc}
\usepackage[english]{babel}
\usepackage{sectsty}
\usepackage[margin=1in]{geometry}
\usepackage{braket}
\usepackage{amsmath}
\usepackage[demo]{graphicx}
\usepackage{subcaption}
\usepackage{float}
\usepackage{tikz}
\usepackage{lipsum}
\newenvironment{outdent}
{\list{}{\leftmargin-1cm
\rightmargin\leftmargin}%
\item\relax}
{\endlist}
\begin{document}
\section{See last part of this section}
\lipsum[1-8]
\noindent\makebox[\linewidth]{\rule{0.5\textwidth}{1pt}}
\textbf{\large{And then there is some more text which I made large and bold here so you wont miss is. The important thing is that there is a paragraph right before the figure, and I don't what that to leave a pretty much empty page as it has here.}}
\begin{figure*}
\vspace*{-50pt}
\begin{outdent}
\centering
\makebox[1\textwidth][c]{
\begin{subfigure}{1.2\textwidth}
\begin{tikzpicture}
\node at(0,0) {\includegraphics[width=0.5\textwidth]{x}};
\node at(0.5\textwidth,0) {\includegraphics[width=0.5\textwidth]{x}};
\end{tikzpicture}
\caption{\textbf{\large{All captions to this figure are really long, and at you can see they don't fit into the page.}} Readout spectra of the transitions from $\ket{\pm 5/2 g}$ to all three excited states and the transition $\ket{\pm 1/2 g} \rightarrow \ket{\pm 5/2 e}$ at 4 MHz in the spectra. (left) The three peaks corresponding to the transitions $\ket{\pm 5/2 g} \rightarrow \ket{\pm 1/2 e}$, $\ket{\pm 5/2 g} \rightarrow \ket{\pm 3/2 e}$ and $\ket{\pm 5/2 g} \rightarrow \ket{\pm 5/2 e}$, positioned at 0, 2 and 6 MHz respectively, are present as expected. However, there is also a peak at $\ket{\pm 1/2 g} \rightarrow \ket{\pm 5/2 e}$ at 4 MHz. This comes from some unwanted ion class, and must therefore be some other transition than $\ket{\pm 5/2 g} \rightarrow \ket{\pm 1/2 e}$. (right) After burning at $\ket{\pm 5/2 g} \rightarrow \ket{\pm 1/2 e}$ the two first peaks disappear. The last one, corresponding to $\ket{\pm 5/2 g} \rightarrow \ket{\pm 5/2 e}$ is still there, although somewhat smaller. This means that also in this peak there are unwanted ions from some other ions class. The peak at $\ket{\pm 5/2 g} \rightarrow \ket{\pm 1/2 e}$ is still there and has become bigger, as expected.}
\end{subfigure}}
\makebox[1\textwidth][c]{
\begin{subfigure}{1.2\textwidth}
\begin{tikzpicture}
\node at(0,0) {\includegraphics[width=0.5\textwidth]{x}};
\node at(0.5\textwidth,0) {\includegraphics[width=0.5\textwidth]{x}};
\end{tikzpicture}
\caption{Another really long caption. Readout spectra of the transitions from $\ket{\pm 5/2 g}$ to all three excited states and the transition $\ket{\pm 1/2 g} \rightarrow \ket{\pm 5/2 e}$ at 4 MHz in the spectra. (left) The three peaks corresponding to the transitions $\ket{\pm 5/2 g} \rightarrow \ket{\pm 1/2 e}$, $\ket{\pm 5/2 g} \rightarrow \ket{\pm 3/2 e}$ and $\ket{\pm 5/2 g} \rightarrow \ket{\pm 5/2 e}$, positioned at 0, 2 and 6 MHz respectively, are present as expected. However, there is also a peak at $\ket{\pm 1/2 g} \rightarrow \ket{\pm 5/2 e}$ at 4 MHz. This comes from some unwanted ion class, and must therefore be some other transition than $\ket{\pm 5/2 g} \rightarrow \ket{\pm 1/2 e}$. (right) After burning at $\ket{\pm 5/2 g} \rightarrow \ket{\pm 1/2 e}$ the two first peaks disappear. The last one, corresponding to $\ket{\pm 5/2 g} \rightarrow \ket{\pm 5/2 e}$ is still there, although somewhat smaller. This means that also in this peak there are unwanted ions from some other ions class. The peak at $\ket{\pm 5/2 g} \rightarrow \ket{\pm 1/2 e}$ is still there and has become bigger, as expected.}
\end{subfigure}}
\makebox[1\textwidth][c]{
\begin{subfigure}{1.2\textwidth}
\begin{tikzpicture}
\node at(0,0) {\includegraphics[width=0.5\textwidth]{x}};
\node at(0.5\textwidth,0) {\includegraphics[width=0.5\textwidth]{x}};
\end{tikzpicture}
\caption{A this really long caption. Readout spectra of the transitions from $\ket{\pm 5/2 g}$ to all three excited states and the transition $\ket{\pm 1/2 g} \rightarrow \ket{\pm 5/2 e}$ at 4 MHz in the spectra. (left) The three peaks corresponding to the transitions $\ket{\pm 5/2 g} \rightarrow \ket{\pm 1/2 e}$, $\ket{\pm 5/2 g} \rightarrow \ket{\pm 3/2 e}$ and $\ket{\pm 5/2 g} \rightarrow \ket{\pm 5/2 e}$, positioned at 0, 2 and 6 MHz respectively, are present as expected. However, there is also a peak at $\ket{\pm 1/2 g} \rightarrow \ket{\pm 5/2 e}$ at 4 MHz. This comes from some unwanted ion class, and must therefore be some other transition than $\ket{\pm 5/2 g} \rightarrow \ket{\pm 1/2 e}$. (right) After burning at $\ket{\pm 5/2 g} \rightarrow \ket{\pm 1/2 e}$ the two first peaks disappear. The last one, corresponding to $\ket{\pm 5/2 g} \rightarrow \ket{\pm 5/2 e}$ is still there, although somewhat smaller. This means that also in this peak there are unwanted ions from some other ions class. The peak at $\ket{\pm 5/2 g} \rightarrow \ket{\pm 1/2 e}$ is still there and has become bigger, as expected.}
\end{subfigure}}
\caption{And a caption for the whole figure. Readout spectra of the transitions from $\ket{\pm 5/2 g}$ to all three excited states and the transition $\ket{\pm 1/2 g} \rightarrow \ket{\pm 5/2 e}$ at 4 MHz in the spectra. (left) The three peaks corresponding to the transitions $\ket{\pm 5/2 g} \rightarrow \ket{\pm 1/2 e}$, $\ket{\pm 5/2 g} \rightarrow \ket{\pm 3/2 e}$ and $\ket{\pm 5/2 g} \rightarrow \ket{\pm 5/2 e}$, positioned at 0, 2 and 6 MHz respectively, are present as expected. However, there is also a peak at $\ket{\pm 1/2 g} \rightarrow \ket{\pm 5/2 e}$ at 4 MHz. This comes from some unwanted ion class, and must therefore be some other transition than $\ket{\pm 5/2 g} \rightarrow \ket{\pm 1/2 e}$. (right) After burning at $\ket{\pm 5/2 g} \rightarrow \ket{\pm 1/2 e}$ the two first peaks disappear. The last one, corresponding to $\ket{\pm 5/2 g} \rightarrow \ket{\pm 5/2 e}$ is still there, although somewhat smaller. This means that also in this peak there are unwanted ions from some other ions class. The peak at $\ket{\pm 5/2 g} \rightarrow \ket{\pm 1/2 e}$ is still there and has become bigger, as expected.}
\vspace*{-5pt}
\end{outdent}
\end{figure*}
\section{Then I tried the geometry package, please read the last paragraph also here}
\lipsum[1-7]
\vspace{100pt}
\noindent\makebox[\linewidth]{\rule{0.5\textwidth}{1pt}}
\textbf{\large{The geometry package has worked best so far.}} Then I can make the figure fit by changing the top margin. However I still have the
\begin{figure*}
\begin{outdent}
\centering
\includegraphics[scale=1]{x}
\caption{Let's skip the figure as you now know why it is too big.}
\end{outdent}
\end{figure*}
problem that the figure does not fit nicely within the paragraph, but a lot of white space appears. I tried to avoid this by placing the figure exactly where I wanted it within the paragraph. As you can see, the paragraph is broken by the figure, which does not seem to be allowed to float and just change the geometry of the page it happens to appear on. Do you see my problem?
\section{Then I tried to avoid the breaking of the paragraph, at least visually}
\lipsum[1-6]
\vspace{120pt}
\noindent\makebox[\linewidth]{\rule{0.5\textwidth}{1pt}}
So I tried to visually make it seem as there was not break in the paragraph by using the \textbackslash newline and \textbackslash noindent commands, but as you can see, this gave me an entire blank page before the figure which I \newline
\begin{figure*}
\centering
\includegraphics[scale=1]{x}
\caption{I've been using the starred figure because I want the figure to span the entire page, as I have a twocolumn environment otherwise.}
\end{figure*}
\noindent don't know how to get rid of!
I hope my question(s) are more clear now. And I am sorry for all the messy code, but I do think it is essential for understanding my problem. I hope you can help me. :)
\end{document}
Best Answer
Wihouth figuring that you are trying to do exactly is hard to say, but except form small chunks of text is just a bad idea make that the end of line (EOL) equivalent to
\\or\newline.I now that in the it is boring at first, but my suggestion anyway is learn What is the difference between \newline and \\?,
\linebreakand\par(See also Downsides of using \par instead of two new lines ) and then just use blank lines to make new paragraphs (not to make new lines) and as less as possible the line breaking commands (in the end of rows of tables ... and no much more.) since probably there are better ways to obtain what you want without any\\. (I am thinking in lists, boxes with text, etc.)Said that, in addition to
obeylinesenvironment, another options areparse linesandverbatimenvironments. What is better depend of what you want, because the tree environments have several significant differences, as you can compare in this example: