Whenever you Boolean you actually create a new object. This is the object you would use if you wish to Boolean again, not the original. Box B is taken away from Box A, this gives you Boolean Surface C or something like that. To take away Box C from that you must choose the Boolean Surface and not Box A again. Hope this makes some sort of sense, and you must keep the original objects or you will lose everything. I just create a folder called Boolean trash and throw the items that have been used up into it. One nice thing about the booleans, you can select them, and then use one of the transform tools to affect the surface. So if you had cut a hole out of a box and decided it was too small, you can select that Boolean, then use the scale tool and the opening will grow
Red bellows of flame have blackened my stones
Convulsing my frame and cracking my bones
Hell's dragons of steel who roar in their chains
Crawl into my caves to suck out my veins.....
-The Mountain P.F.M.