I think you're on to something if you're concerned about using a 3TB drive as your boot drive (I'm taking that's what you mean when you say Master HD).
Because BIOS is legacy software, it has issues identifying HDDs larger than ~2TB. I believe what actually occurs is the HDD is recognized, but the size of the drive is truncated to the maximum BIOS can recognize.
I found THIS ARTICLE
which provides some detail. In the article it states: "you can boot Windows from a 3TB drive only if it's 64-bit Vista or 64-bit Windows 7--and then, only if you have a PC with an EFI/UEFI BIOS.
I looked at ASRock's website for the motherboard
you mentioned and I do not believe it has the newer BIOS. Perhaps, someone else can confirm.
And I should warn you that one other frustrating thing I noticed with larger HDDs is that Windows 7 cannot use the drive for backup & restore process (this has to do more with the way Win7 saves data as opposed to the mere size of the drive).
Now, all is not lost. You can use the drive as a storage device. And while I haven't tried it, you may be able to partition the drive and use one part as your boot drive and the other as a "D" drive.
Hope this helps.