It was only a couple of years ago that I discovered the 'Select Files' command in Rev Manager.
Don't forget you also have 'Deselect Files', and also Find and Replace.
I use these regularly for renaming a whole load of files, such as for a previous customer who copied models and drawings for each new project - the project code, machine code etc was changed for each new set, so it was an easy replace XXXX with YYYY.
It really is worth getting to know rev manager - once you get the hang of it it's really powerfull. The only real way is to practice on dummy files first.
As for superslinky's original question, I would always keep models together and not seperate them into assys & parts.
It can be a good idea to keep drawing seperate though.
bc.
2.4GHz Core2 Quad, 4GB RAM,
Quadro FX4600.