Not familiar with the specific controller, unless it happens to be the Intel MegaRAID...
You often have to specifically set an array bootable in the raid config.
Need a bit of clarification though. What Windows are you installing? It makes a big difference as far as whether the RAID drivers should already be there. Windows 7 recognizes pretty much everything. Vista I haven't messed with much. XP doesn't recognize ANYTHING and you'll need a driver disk.
If the Windows installer can see the array but refuses to install to it, the drivers are there but there's some other problem.
I always recommend that people do not boot to their RAID arrays. In the case of a RAID-10 I'll loosen that recommendation a little bit, because the failure scenario is fairly unlikely. My recommendation is because of the behavior of the RAID controller if a bad block is encountered:
Single Drive: Windows hiccups for a bit but reports the bad block in its event manager and continues on.
RAID array: If a RAID disk times out, that disk drops from the array. If there is no redundancy at the time, it drops the entire array immediately. This causes an instant blue screen and reboot in Windows and since the array has been dropped you don't get any events in the event viewer. The next time you boot windows it has no idea what happened, for all it knows it lost power.
A disk can drop from the array because of a bad block on a disk, or because the disk is not meant for RAID and goes through a longer than normal self-service cycle. Depending on the controller and the type of disk, it may try to move the bad block and continue. If you are using WD Caviar Black disks, make sure you have used the TLER utility to set the Time Limited Error Recovery bit on the disks, that prevents the disks from timing out as easily. (Does not make them 100% as good as buying Raid Edition disks though.) If you are using Seagate, I don't know if it's possible to fix the error recovery timing. I had a raid-0 array of five 1TB Seagate drives, two months old, and it would time out constantly. (I think one of the disks was legitimately bad though.)
This is on top of the fact that installation is easier, and you don't have to worry about a driver update or a raid card bios flash preventing you from booting.
In your case, with Raid 10, I think you're pretty safe as long as you have either Raid Edition disks or WD Caviar Black disks with the TLER bit set. If you do get Windows installing though, I highly recommend making a single-drive-sized (500GB to 1TB) partition for the OS. That way if you have difficulty booting at any point, you can use a Linux boot CD to image the RAID boot partition onto a single drive and get your OS back.