Sidenote: Good choice with the Apogee Duet 2. It's my favorite bit of kit and was worth every penny...especially with regards to its preamps when it comes recording guitar, vox, etc.
Since you're building a computer and using the Duet 2, I'm assuming you're building a Hackintosh (Apogee only bonds with Apple machines)? Would love to hear about your build as I would like to make my own Hackintosh desktop one day...I'm just a bit busy to put in the effort in figuring out what specific components to buy in order to "trick" OSX into thinking it's a factory built Apple machine.
Shoot, I didn't think about the compatibility with windows!!! I was planning on adding my ssd and hd from my mac (the case I'm getting has 5 hard drive slots) and occasionally running that. But, I'm really looking to start working with FL Studio and was building this mostly as a system for that; also I'm learning a 3D projection mapping program (read: MASSIVE HD video files in 3D, etc..) called TouchDesigner that's windows only and can interact with Ableton and do crazy real time audio-reactive video http://vimeo.com/49983069#at=0
I'll be so swoll' if I have to go back to my.....m-box mini
Gotcha, so essentially you want to build a Hackintosh equipped with multiple hard drives in order to run a sideorder of Boot Camp so you can mess with FL Studio and other PC progs.
It definitely can be done, it's just a matter of purchasing the proper components (motherboard, chipset, etc.) that will fool OSX into thinking it's a legit Apple machine. I think I have a couple helpful links if you're interested.
It's a downer that Apogee is Mac only, but understandable since their products are all built around CoreAudio foundation...but yeah, you'll probably have to alternate between the Apogee Duet 2 and m-box mini.