I think you must first understand the TeX/LaTeX typesetting system. TeX and its offspring PdfTeX, XeTeX, LuaTeX, etc. are programs that interpret a specific markup/macro language to create a high quality printable document format. TeX's power resides in its line, paragraph, and page breaking algorithms for pieces of text and its power to typeset mathematics.
TeX itself is not very friendly, therefore macro packages was created to work on top of it. The most basic one is PlainTeX that has a few basic macro's and the user must do most of the stuff directly (references, counters, etc.). This is what Donald Knuth the creator of TeX uses to write his series of books.
Later more comprehensive macro packages such as LaTeX, ConTeX etc. were developed that use TeX as a base to output beautiful documents. A lot of support software was also created, such as BibTeX, Metafont, Metapost, etc. The LaTeX distributions such as MiKTeX and TeXLive consists today of TeX/LaTeX interpreters, the base macro and class files and thousands of user contributed packages and programs.
LaTeX code is normal text file that can be edited with any text editor, but a number of IDE's are available to help with the typing of a LaTeX code. There are for instance buttons to insert code and to run the TeX/LaTeX interpreters, etc.
TeXnicCenter is one of these IDE's. You can also look at others such as TeXworks, TeXmaker, TeXmakerX, Winshell, WinEDT, that are doing more or less the same thing. You need to know your LaTeX well, because you are working directly with the code and have to do all the markup yourself.
LyX employs a different approach, using TeX/LaTeX as a typesetting engine and showing something of how the output will look. It is still not WYSIWYG. It just hides most of the markup from the user, but in the process the user also looses most of the low-level control. It is a great program with lots of users, but you still need to know a little bit of LaTeX to do anything more than a simple document.
In conclusion TeXnicCenter, and LyX are two totaly different system that cannot be compared directly. At all depends on how deep you want to get involved with a documents's markup. The LaTeX purist will not touch LyX, while the LyX fanatics would say that anyone who want to suffered with direct LateX code is mad.
You can set your preferences by going to Tools/options/spelling and then you'll find some checkboxes and select the ones you want to ignore.
The menu looks like this:
For more information on these options and others, please visit the TeXnic Center's optionsdocumentation
However, please bear in mind that ---as stated in the documentation---, the argument of the command is always spell-checked, and not the command itself.
Furthermore, if you wish to include this feature for specific commands (such as \label and \ref) in future TeXnicCenter versions, please add your recommendation in the TeXnicCenter Feature Request Page
Nevertheless, there is kind of a workaround: as you can see in the picture attached, you can ignore things with numbers and/or uppercase... so you can always use numbers and/or uppercase for the arguments of \label and \ref and \cite.