An axes is a portion of a screen within which you can put graphics. You would not often want to change the size of your axes as the program runs, but you might change the size of something you have drawn in the axes.
I suggest you consider using a single axes, and two rectangle() commands that represent the outside of the fuel tanks, and two filled rectangle() commands that represent the volume or heat.
It is not possible to run multiple MATLAB graphics command simultaneously. Even if you had the Parallel Computing Toolbox, or were to spawn additional Java processes, all MATLAB graphics is forced to go through one single thread in order to prevent inconsistencies in the graphic structures. Instead, update the graphic objects sequentially. MATLAB only updates the screen under limited circumstances, so even though the instructions might be given sequentially, the combined result of the instructions is most likely what will show up on the screen on the next screen update.
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