For the most part, my understanding is that external hard drives do not play well with both PCs and with Macs -- you sort of have to decide in advance which way you are going, because the hard drives have to be formatted differently for the two operating systems. So you may want to get the hard drives and the Mac Mini all at the same time, and do this all at once.
Assuming you have either Snow Leopard or Lion set up as the operating system on your Mac Mini, what you propose to do is relatively straightforward.
First, you should select hard drives that use the Firewire 800 interface (Apple sells several 3T models with Firewire ports, from various manufacturers, through its online store and in its retail stores). You can connect the drives to the Mac Mini "in series" following the instructions that come with the drives themselves. Both will be visible on your desktop.
Then, copy your iTunes library to one of the external drives (to move it from a PC, you may have to either use a network connection or burn your iTunes library to a DVD-R, or purchase PC-to-Mac conversion software -- I'm not sure what the right approach will be -- the Folks at Apple's Genius Bar can help)and then re-set iTunes on the Mac Mini to recognize the copy on the external drive as your iTunes library (there are instructions on how to do this available through Apple's online support -- or, once again, you can get instructions from the good folks at Apple's Genius Bar). When you add new music to iTunes, it will be installed on the copy in your external hard drive.
Then, set up Time Machine to use the OTHER external drive as your Time Machine backup drive, and configure it to back up the iTunes library on the first external hard drive as part of the Time Machine backup process (this is easy to do using the Time Machine software interface on the Mac Mini).
While I'm not using 3T drives, this is exactly the setup I'm using at the moment for my photo library, which had gotten too large for the hard drive in my MacBook Pro. I have the libary on one external hard drive, and then have both the MacBook Pro and the photo library being backed up onto a second external hard drive using Time Machine. Works just fine.