I don't think it will be a problem if you get a good controller card. The ones from Promise Technology state they are compatible with linux:
http://www.promise.com/product/pdquide_eng.asp
If your not interested in doing a raid configuration, it should just work in a recent linux distro, certainly in mdk 10.1. In fact, your likely to have more trouble getting windows installed on it. That's what I found when I upgraded my mb with an on board(intel) sata controller. I wound up leaving windows on my old pata drive because of the hassle.
Re how sata drives are designated in linux, that depends on the kernel. All the recent 2.6 kernels designate sata drives as scsi hard drives, i.e. /dev/sdxx. The older 2.6 kernels designated them as /dev/hdex. There was a lot of kernel work on sata over the past year and I would definitely go with the newer 2.6 kernels; sata support is greatly improved by the newer kernels. All the current releases of the big distros(mandrake, suse, fedora) are using 2.6 kernels that designate sata drives as sdxx.