Need help organising my disks

OK, I'm sure after this I'm going to get a lot of replies lecturing me on organisation and you'll all be right!

When I first installed Final Cut I just dived in there and so my folders are all over the place and I need to organise them.

I have 3 drives 2 internals and 1 external, they have all been my scratch at one point or another, but it's the organisation of my boot and 2nd drives that I need help with.

I now have a situation whereby my 2nd drive (internal) is my scratch disk and I have a folder called Final Cut Documents which holds all my most recent render files and is the one in use at the moment.

My problem is, through my earlier disorganisation I've now got duplicate folders, which I'm not entirely sure I can delete.

So on my 2nd drive outside of my Final Cut Documents folder I have a capture scratch folder, with some old files in it; can I move these files and delete the folder?

Also outside the FCD folder I have a Waveform cache folder, audio render files and auto save files folders, all of which are empty; can I delete all these folders?

Lastly I have a thumbnail cache folder, containing 2 old files and a render files folder containing a constant frames folder with some old files in it? Can I move/delete the files then delete these folders?

Moving to my boot drive now I have a Final Cut Pro Documents folder contaning all the same folders as above, most of them contain (old) files, especially the waveform cache folder which has a number of files in.

Is it OK to move/delete these files and folders?

Sorry if it's a bit of a silly question, but I thought I'd better ask before wiping stuff, many thanks in advance.

aka Newbie Wan Kenewbie. "I will get over my manualaphobia, one day at a time."

System
Mac Pro 2.8Gb quad core
8Gb RAM
1x 320Gb 7200 hardrive
1x 1Tb 7200 hardrive
Nvidia Geforce 8800 512mb Graphics card
1x 1Tb external WD 'My Book' eSata

Equipment
Panasonic AG-HVX 200
Firestore FS-100