Hi otterkins2.
I'll run through the way I dio things and explain why.
I have a wireless network of 3 PCs a Laptop and a Windows mobile HTC XDA
the basic setup on any will be
C: drive ( partition on HDD 0 of aproximately 100GB ) This contains the OS and system specific security such as Norton 360 and Spybot anti-spyware and very little else. I cannot stress the importance of allowin as much free space as possible on the partition that contains the OS, XP or Vista will benefit greatly from this space.
D: drive (partition of HDD 0 remaining space ) This will contain my program files ( This is where my CS3 suite, 3ds Max, Poser 7 etc live )
E: drive ( Partition of HDD 1 size varies ) this will contain my gaming software installations.
F: drive ( partition of HDD 1 remaining space ) this will contain my backups and usually the rest is empty for moving large files and temporary extraction of huge archives.
G: H: I: drives , these are 3 external 320GB HHD and this is where all my downloaded files go including torrent hash files and the resulting downloads. Also one of these contains my scratch disks for my CS3 applications. This is VERY important.
Now, I don't use p2p clients of the Gnutella variety but I'll not get into why it is a personal choice but should you choose to there is no reason why you can't put them all onto your D: partition in a shared folder location, in fact this is preferable, just instruct your client as to where the shared folder is located. If you do use Gnutella based p2p clients then you should not share your default music, pictures and document folders. This gives you greater security of the files you wish to share and more importantly those personal files you do NOT wish to shareI Use Usenet and downloads go to my external drives.
I use UTorrent and specify 3 download folders ( games, apps, other ) on my external drives. It does not matter where your downloaded files live as long as your client is aware of the location there. You should specify a folder on your D drive and use that, but with bit torrent it does not matter where you download your files to ( they can be on many different drives and partitions ) as long as the client knows where it is and it remains there it can continue to share it.
Now a bit of advice if I may? I am a graphic artist and use CS3 a lot. Photoshop and the like require a scratch disk ( this is where it moves data to as you work ) The default settings are to the C: drive. This is a very bad idea as it can seriously limit system performance if you work with many layered image files ( some of my paintings will easily contain over 150 layers and they eat memory and HDD space as you work ). All professional users of Photoshop know that on installation you should specify that it uses a scratch disk that is on a separate hard drive ( not another partition on the same drive ) for vast increases in performance. Sadly your configuration as yet does not allow for this but with the advent of cheap large HDD these days you should consider adding a second drive to your system. Either internally or if you are not confident to perform such an installation yourself it is becoming cheaper to simply add an external drive. I added 1TB of space for around £160 from ebuyer.com ( Iomega_HDD 320GB £52+ delivery )
I hope that some of this information has been usefull to you and please do not hesitate to ask further questions and I shall endeavour to impart my meager knowledge to you.