I think you are going to have problems. SME is designed to be a 2-disk (identical disks) software RAID1 system. ie everything on the first disk is mirrored onto the second disk - or a 4 (or 5 or 6)-disk RAID5
A 1-disk SME server is treated by the OS as a "degraded array" - it still runs because that is what it is supposed to do until you replace the "missing" 2nd disk.
You are proposing (I think) to try to develop a SME server with 1-disk for OS and a seperate 2-disk RAID1 for the Ibays. This is not the way SME works, so upgrading will be difficult.
If you have 2 identical SATA disks, install your server and its Ibays on them and let it run as a mirrored RAID1 system as it is designed to be.
If you want to have 3 disks, it will be installed as a RAID1 system with a "spare" disk. Some people use this spare as a backup by swapping out one of the active mirrored disks and replacing it with the 3rd disk (I think you have to erase Disk 3 before you do this, but I am not sure) and making this a weekly practice, so you have an active RAID1 2-disk system and a spare disk with last week's system and data on it in case of emergencies. If you want to try this THE 3 DISKS MUST BE IDENTICAL IN SIZE. They can be IDE and SATA mix.
Remember, if you deviate from the standard system and tested addons/contribs,
1) you are on your own as far as help goes AND
2) it may (probably will) get clobbered when there is a software update anyway.
I suggest you read the documentation on RAID :
http://wiki.contribs.org/RaidI also suggest you read the rest of the Administration manual :
http://wiki.contribs.org/SME_Server:Documentation:Administration_Manual so you can get a better feel of what SME is about and how it works.
Cheers
Ian