Sorry to be so abrupt, but RTFM.
Don't just launch yourself into a new distro and expect it to do what you think...
SME is a tightly controlled, idiot-proof (nearly) system. It expects you to have 2 identical size drives and it automatically makes them RAID1.
If you only have 1 drive, it considers it a "degraded" RAID1 array.
If you have 3 (identical drives) it still makes it RAID1, but one is a hot-swap spare.
You have 3 different drives....expect the unexpected; cross your fingers and reach for the OFF button.
My guess is that it tried to make a RAID1 array based on your 2Gb disk.
If you want the 40Gb disk as a data drive, search the forums on how to add another HDD. It's not difficult, really.
BUT --- the best thing to do would be to get another 40Gb drive and just use the two of them as a RAID1 system - SME +DATA on the same disk - after all, SME does not take up that much room. This would give you better redundancy in case of HDD failure.
And get rid of the 2Gb and 3Gb disk - they are almost door-stop material these days.
Cheers
- and good luck.
Ian