Putting a SATA II drive (or even 3) on an original SATA (I) controller MIGHT work with no intervention, or you might need to do a little tweak. Some new SATA drives are smart enough to figure this out and slow down to SATA I speed. On the other hand, several drive makers provide a way for you to force your SATA II drive to run at the slower speed. Seagate and WD, I believe, do this with a jumper on pins, a bit similar to the jumper system used for setting Master etc on IDE systems. (BUT these do NOT set up a Master or Slave!) Other makers may provide a software tool you use to write a setting into the drive's board's PROM. Check details of how you can do this if necessary from the maker's website BEFORE you buy.
Using a drive connected through an add-in controller board on the PCI bus as your boot drive may be done two ways. Some controller cards have a BIOS that can integrate with the mobo BIOS so that all the system resources appear to the OS as just part of the whole system. To do this you also need a mobo BIOS that is designed for that. You need to check details with both your controller card and your mobo makers to see if this can work for you.
The other way is, as wathman says, you can load the necessary driver into Windows XP SP3 at the right point when you are INSTALLING it. That way the driver becomes part of Windows and it can use the drives for anything, including booting. But, as wathman says, XP ONLY can load this from a Floppy disk during the Install process.
The related issue is - it's SATA! Windows XP only knows how to deal with IDE HDD's. One way recent mobo BIOS's avoid this is to have the disk controller in the BIOS Emulate an IDE drive for an actual SATA drive, so Windows does not know the ugly truth. But your add-on controller card may not have that capability. To use a real SATA drive in Windows you need to install a driver, by that same process during the Install routine.
Bottom line looks like you will need to do a fresh install of Win XP SP3 to your new SATA drive connected via a PCI card, and during that you probably will need to use a floppy disk to install at least two drivers - one to gain access to the PCI controller card, and a second to let Windows build in SATA device use so that it can boot from that device. All that means, of course, that you need to find those divers from the controller card manufacturer and get them onto a floppy disk before starting. Oh, I've presumed you have (even temporarily) a floppy disk drive in the machine?
By the way, if you set it up as you plan, do NOT get confused between IDE Master and Boot Drive. Any IDE channel MUST have one device jumpered as the Master for that channel, and may also have a Slave on the same port / cable. This has NOTHING to do with which drive unit is your boot drive - that part is set separately in the BIOS. So, even though you boot from a SATA drive on a PCI card, the IDE drive will still have its jumper set to be the Master of its channel.