I keep different databases for different poker sites so that I do not have one overly large database. I also like to keep separate databases for different types of game e.g. 6 max vs SNGs. It makes searches quicker and easier.
I would like the ability to assign auto import folders to each database, rather than as it is at present i.e. when I switch database, I have to change the auto import folders. When I forget to do this, I have databases with hands from different sites and different kinds of game and it is a mess to clear up.