In normal opereation, the first place SE looks for parts when opening an assembly is in the same folder as the assembly.
So if you have 2 part files with the same name, one in the assembly folder, one in a different folder, SE will not use the one in the different folder. You will also not be able to use this one in a 'Replace' command, whether in the Assembly or in Rev Manager.
If the parts are in different folders to the assembly you will still not be able to do a 'Replace' in the assembly, but I think will be able to do the replace using Rev Manager.
Hope this makes sense.
As Scott says, using the LinkManagement text file may change the way things work, but I wouldn't advise it.
You shouldn't really have 2 files with the same name anyway.
bc.
2.4GHz Core2 Quad, 4GB RAM,
Quadro FX4600.