I am modeling on a set of windows right now, and they are not symmetrical along the X axis, where I need the mirror modifier to mirror the other half of the superstructure. This is what it looks like. The problem basically arises when I need to make the windows non-symmetrical across the mirror.
One possible way would probably be to apply the mirror, make the adjustments, then separate the windows from the main superstructure and finally joining them with the superstructure afterwards?