A common "best" way to set up RAID volumes with only 6 spindles is:
- Volume 1, operating system and SQL transaction log. 2 disks in mirror (RAID1) with BBWC. Write caching of the transaction log is very important for good performance, as the SQL engine waits for log writes to complete, and caching the writes reduces write latency significantly. (BBWC means Battery Backed Write Cache, i.e. a controller with write caching turned on and a battery backup unit attached to the controller.)
- Volume 2, remaining Database files. 4 disks in RAID 10 (or RAID1+0, or RAID 0+1).
The placement of the OS really doesn't matter so much. When the system is up and running, the OS should gradually enter a steady state where the OS is only occasionally touching the disks. If you need to put the OS on the 4-disk RAID 0+1 array, then don't worry about that.
Additionally, you must ensure that partition boundaries (and hence filesystem blocks) are aligned with RAID stripe boundaries.
The above setup may or may not work for you -- you will lose some capacity when you say goodbye to RAID5. With modern disk drives you probably have disk space enough (I/O per second often becomes a bottleneck before capacity). With older drives, maybe capacity will be a limiting factor.
Kendal Van Dyke has written a good overview of different RAID levels, partition alignments, and their performance for a SQL server workload.