My case comes with 5 hotswappable drives - but in the interest of not messing something up, I use all 5 bays for only the SATA II connected drives, none of which I have made bootable.
I keep both SSDs internal (and not easily accessible) from which I boot only one, using hte second as my \Users tree repository (which then, by default, includes the VDs for my VMs).
If I were to dual boot and use multiple drives, I'd use hte BIOS instead ot adjust boot order. I use my hot swap bays for adding . removing storage based upon what I am doing.