I have 3-1.5 Tb drives hooked up externally to my iMac using FW800. They claim the theoretical transfer rate of FW800 is 786.432 Mbit/st. I have moved massive amounts of data and the transfer times blow me away. I am using Glyph drives running at 7200 rpm and 32Mb of cache, and the transfer rate is 150MB/sec.
You can partition the drives anyway you want to run Time Machine or what ever. It will all work fine.
I would highly suggest you look at Glyph drives. They cost a bit more, but have a superior warranty and are superior drives. They come with a nice carrying case also, and no wall warts.