Are you using all SATA drives? If so, then drive layout is not as important as it had been in the IDE (PATA, or parallel ATA, or non-serial ATA) days.
Ideally, you want to never have source and target on the same drive, if avoidable. Encode video on a D:\ drive, for example, to a new file on the E:\ drive. It's also best to never have anything large or "media" (photos, videos) on the same drive as the operating system.
This also assume the OS is putting its temp/swap files on the C:\ OS drive. Check for that. It's not much help if, for example, Photoshop is storing its cache on the D:\ drive when all your photos/images are also on D:\ -- that doesn't help speed up Photoshop use as much as putting it on another drive. I suggest C:\ for that.
For IDE, not only should data have been on different drives in the IDE days, but on separate IDE channels. Motherboards generally only had two IDE channels, so more advanced video computers (like mine) often needed PCI expansion cards to add more IDE channels.
It always comes down to bottlenecking of data. Sometimes that happens are CPU or RAM, yes, but sometimes it is most definitely an issue of the drives.
Drive cache, drivers, motherboard hardware/software, drive speeds, and other related issues can also impact drive performance. For example, I have one computer that works perfectly when burning DVDs, any IDE channel, while another will only burn well from the SATA connection.
Hope that helps. If further questions, ask.