There should be no issue saving QVDs to three different locations (and reading them from three different locations). Unless your QVDs are very large or they aren't read in an optimized manner, you won't likely see any major changes to performance, since an optimized read from a QVD is quite fast in the first place.
Insofar as which file goes where, you'd probably need to supply that logic on your own. I don't think Qlik tracks how often QVDs are read other than in each app's individual reload log, though there may be other ways to track this that I'm not familiar with.
