Maximum PC

After having several computer issues this summer, my sister has decided on upgrading her motherboard to an ASUS M4A79 Deluxe (yeah, I know its over three years old but she wanted to keep her AM2 processor and her DDR2 800 MHz memory that she had in the previous board). Since her 500 GB hard drive that she wanted to use for the primary hard drive bit the dust, she purchased a new WD 1TB Caviar Black SATA III hard drive to take its place, but she wants to use a 320 GB WD Caviar Blue SATA II hard drive in an external hard drive enclosure via the e-SATA port on the ASUS motherboard. I am aware that I will have to install the AHCI drivers (she is running Windows XP SP3 as her OS) for her motherboard during the OS installation, and that I will need to run WD Alignment software after the OS installation. If she decides to install a PCI Express SATA III controller card later on (to take advantage of the SATA III speed capabilities of this new drive, what would be the proper procedure to follow and still allow her to use her external drive through the mobo's e-SATA port?

1. Hard drives don't need alignment. SSDs do, if you want to boot from them with XP.
2. SATA is forward and backwards compatible
3. You're not going to see a performance hit if you put that hard drive on a SATA I, SATA II, or SATA III port. The throughput on hard drives has yet to surpass what SATA I offers.

In other words, carry on. You don't need to do anything special beyond setting up Windows for AHCI.

EDIT:
Actually, you need to align hard drives if you're running them in 4K mode.

Thanks for the information in your reply, LatiosXT. That is good to know.