Need a little more information.....
Are you using hardware RAID or a form of software RAID?
If this is hardware RAID, it shouldn't mess with anything, be sure to add the drivers for both RAID controllers by pressing F6 during the beginning of setup to add mass storage controllers.
When you're selecting what partitions to blow away/format, check and double check what you're doing..... don't wanna blow away the partition on your IDE RAID by mistake. If you have any incling of making a mistake, back up your data to CD-R or DVD-R prior to rerunning setup.
If on the other hand you're running Software RAID controlled by windows, the disks will be lost because of software disk signatures.
Good Luck, feel free to email me if you want more detailed info!