Ideally you want your system disk (usually C and your log files disk (usually D on 2 RAID 1 arrays and then your database on a RAID 5 (E: drive). This keeps your log files and database on separate disks allowing the system to write to both at the same time increasing performance. With 3 disks, you can't achieve this so it doesn't really matter, but I'd split it into 3 partitions anyway just cos I'm like that!
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