Partition structure?
 

I have two harddrives. One is a 200GB that's partitioned into a 50GB C: for Windows and Program Files, a 150GB E: that's for editing software and project files (video captures, rendered files, etc) and a 160GB drive that's for media (music, TV shows, movies) and occassionally project files, if the E: gets too full.

Is this a good setup or should the C: have all my software while the E: has just project files?

Operating systems (and sometime applications) have to do all sorts of housework. They do this at various times and if you are working on something and the hard drive head has to move from partitionA to partitionB and back again repeatedly, it can really slow things down or cause interruption to your data flow (dropouts, clicks/pops in audio, etc).

Best thing to do is have separate dedicated drives.

Drive C with OS and applications
(a separate partition for the OS is great but not neccesary, does make backups/restores easier tho)

Separate drive for projects and data

More (or external) drives can be added for more room.

Drives are SO cheap these days (I used to pay $3000 for a 9Gb drive...) that it just better to have more of them rather than use partitioning.

I agree with Tim - The way to go is to keep all the OS stuff on a separate drive to the media. Also make sure if they're EIDE that they're on separate controllers (rather than primary and slave on one controller). This means both have a dedicated route to the motherboard, rather than sharing a channel.

If necessary, your CD/DVD drive could share a channel with either drive.

Hope this helps