So apparently, not all mobos support booting from mSata. But I guess the proper way to do things is to go into intel rapid storage and disable the msata cache acceleration. In the bios, switch the msata drive to AHCI mode. then you should be able to install the OS on it and have it boot properly.
It doesnt hurt to remove all of the drives, add your empty msata drive, attach the USB stick (with OS), and see if you can load the OS. Wont take long. Thats the easiest way to find out for certain