Sata Raid question/opinion

I've just updated my server motherboard with something a little newer and faster and I'm setting it up for extra redundancy and just wanted opinions of what people think is best and why.

My server is a P4 3.6Ghz, 3gb DDR2 600 and functions as a bunch of things, amongst which will be a file server. For the file server side of things it has an Adaptec 3085 controller which I will be putting drives in Raid 6 for large capacity+redundancy. For the boot side of things (And where important data will be saved) I will be utilizing 2 x 750gb drives in Raid 1 as well as having daily backups. My question to people reading this is:

Do you think it would be best to use Windows Dynamic Disk or the built in Silicon Image Sil3114 for my Raid 1 and why?