Is there a suggested directory structure for iTunes?

Is there a suggested directory structure for iTunes? I have moved my library around several times (what with new machines, etc.) and I find that I have two app libraries in different locations and I think it is the problem behind a refusal to sync issue I'm having with my iPad.
Any help would be gladly appreciated!
Luke
(Screen grabs a great help)

I'll see your Tb and raise you some - the truth is, almost every major revision and data migration from MBP to MBP and now back to a MP has caused replication of folders in the strangest of places, none of which I have consciously created - I mean, why would anyone except out of self-focused spite want to create three different sets of apps folders - to say nothing of the interminable Compilations folders that sprout from no where in particular!
I could understand the issue if I was careless or a complete neophyte,  I only moved to the Apple platform about 6 years ago, (even though I've been using the platform since 1987) when I went to work for the company.
iTunes I think is a little like a cat - it recognises my lingering, subyle antipathy and rolls all over me just to mess with my head!
Thanks for the information, none-the-less, greatly appreciated.

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