I posted about raid setups a few months back.
Basically, you have to determine where you want your speed:
1) Large (1 gig or greater) file transfers
2) Small file transfers
3) happy medium
For booting windows, small file optimization is fastest. For loading games with huge textures and maps or transferring or ripping movies you want large file optimization.
This optimization is chieved by seting your stripe size. It has been a long time since I set up my raid (2 80gig SATA western digital special editions.) I pulled alot of information from www.storagereview.com
Other than that, make sure that you have a floppy with your raid controller drivers on it prior to formatting and installing windows. You have to hit F8? during the setup initialization in order for the controller (and your new array) to be recognized. Oh yeah, I don't know your depth of understanding, so also remember to hit whatever key it is to enter your raid controller's bios after the POST. From there you can build your array and set parameters such as stripe size. Also make sure that the two drives are matched in performance and capacity, and set as master on each ide (or sata) channel. Do not attempt to connect any other drives to the raid controller channels.
I kind of went backwards here, but let me know any specific questions that you have and I will try to help. Pupp is knowledgeable in this area as well.
edit - read this http://faq.storagereview.com/tiki-index.php?page=StripeSize
