So your building a new computer, or your lucky enough to get a laptop with 2 harddrives, this is for you.
First we have to decide how to backup our files... there are a few solutions:
-RAID 1
pros: automatic, transparent to user, protects against sudden harddrive failure
cons: if you get a virus/corruption, your backup is useless
-Drive Cloning
pros: stable backup
cons: time consuming, often requires computer shutdown
-Manually
pros: stable backup, best performance
cons: requires some setup time
To manually backup your data, partition your drives like this: (assuming you have 2 * 500 GB hds)
Drive(1) Windows (50 GB) | Media (200 GB) | Backup_Games(250 GB)
Drive(2) Games (250 GB) | Backup_WinMedia (250 GB)
This offers the best performance because, when your gaming you are using 2 harddrives at once (loading game files / windows files / listening to music). Also since you are using the first half of the harddrive only, you are "Short Stroking" your drives, cutting the Access Time down and using the top end of Transfer Rate. Hence why 2*500 GB is better then 1*1000 GB!
Here are two images showing the performance
WITH and
WITHOUT short stroking (and thats only my small 250gb laptop drive s.s. to 160gb, a 500 s.s. to 250 is a much bigger difference...)
I use my own backup software to weekly create WinRar archives of my data overnight, storing them on the opposite drives, and I performed one clone of the Windows partition using Acronis Drive Image (as some files are locked by Windows) as a base install. I can post it if someone wants.
Hope that helps someone...