Yes, you can put the OS on the RAID1 array. Note, however, to my knowledge there is no program that can change the cluster size of an NTFS partition if theres is data on it. So if you let W2K or WXP format the array during install (by pressing f6 to install third party drivers) you get the default cluster size of 4k, which may not be what you want.
This is most relavant with a RAID0 array where you want to get the right stripe and cluster size. I dont know if the performance of a RAID1 array can be tweaked this way. Anyway I recommend you use an old third drive to temporarily install the OS and benchmarking tools on. Boot on this drive and set up the RAID array as you wish and format it. Then install the OS on the prepared array. When this is done, you can remove the third drive.