Save and load the selection using the respective menu commands.
Just a thought, heck I don't even know if it would work. But In theory or well...
With two layers you could set the top layer to difference, then in the channels panel alt select or opt select the rgb thumbnail. That should select the differences then if necessary it is a simple matter to invert the selection.
But the proper way besides what Mylenium mentioned, is to use the modifier keys to add, subtract, or intersect selections.
The beauty of the way Mylenium's method is if you make a mistake, you don't have much to do to reselect since it is saved for you and you can retrieve it any time as long as you save the file itself in a format that support alpha channels, such as psd or tiff.