for what you are asking, MC doesn't care where the files are!
the trick is in creating the view properly. for example (and i just did this to verify it all): i have a split album with ash borer and fell voices, each one track. i want to consolidate into a single album (multiple artists) - ash borer vs. fell voices - split EP. for this i put the ash borer track on N: and the fell voices track on Z: (note: both locations must be imported into MC!)
i found both the tracks in an "all music browse" view scheme, select them both (ctrl click). tag as you like...in this case album artist = (Multiple Artists) and all the genre, album, etc tags should match each other
then choose RMC, and select your parameters...in this case i choose
base path = I:\incoming\
rule: [album artist (auto)]\[album]\year
when i press OK, both files appear in a folder titled I:\incoming\(multiple artists)\ash borer vs. fell voices split EP\2010
note that i've used 3 different locations (N, I, and Z) and MC puts them all right where i want them, in the folders that i want them! this trick will work for any amount or type of files that you want...
the trick is to create the view scheme that allows you to easily find all the files, as they must be manually selected. when i did some cleaning of my library i made a custom tag called [fix], then tagged all the files i wanted to see with [fix]=1, then made a view to easily see only those files.
MC only cares where the actual files are ([filepath]) in certain situations, like calling an album "complete"...only an album in a single folder can be called "complete" for example.