When you say stacked on top of each other? Are they all at Elevation 0, and controled with layers? Or are the plans at the elevation they would be beuilt? Are you using ADT? How many users are working on these drawings?
As you can see there a lot of variables to consider.
The way I usually manage a multi level project (using vanilla AutoCAD, ADT is a whole other story) is separate all the floors into separate files, but (and here is the key) with the same insrtion point (ie: 0,0). Then xref all the floors into one master file, only so I can see that they everything is lined up, and inserted with the same coordinates.
I use this method because in the past I have had usually a team of drafters all working on the same project, so this way, more then one person can be working on the floor plans at once.
I guess if you were the only working on these drawings, and you had a good layering system you could put everything in one file.