I have tried both in a SATA raid 6 config and I did notice an improvement using a separate boot disks.
I used two western digital raptors in raid 0 for a boot volume on a separate raid card and then 5 samsung 1tb caviares for the raid 6 configuration.
Give it a go if you have the disks and see if you notice the difference. It makes sense from a ease of use point of view.
hope this helps.