Personally, I like to keep my filing hierarchies as flat as possible. So I wouldn't have "complicated financial forms" as a category, I'd have "2007 taxes," "Boston house sale," or "January trip expenses."
That's what I would do. You might eventually decide that you need parallel systems--for instance if you work on some projects *exclusively* in particular physical or online environments--but in general consolidation reduces the chances that things will get lost.In short, I have 4 seperate GTD systems running each with their individual (and often overlapping) projects, NAs, reference, and maybe somedays! It's the EPITOME of chaos from organization!! haha. I think the best remedy to that convoluted quagmire is to just consider 1 of those 4 electronic GTDs the MAIN system and then just dump all contents of the other 3 GTDs in the inbox of hte Main one.