XP inside an aligned windows 7 machine will be fine, as the disk it would be contained on is already aligned itself.
SATA3_0 is the bottom white port, against the PCB, you can move the drive around safely. You must be in AHCI mode to install the Intel drivers, you will need to make the following changes in windows before rebooting to the BIOS and setting that to AHCI.
Enable switching between all IDE/AHCI/RAID modes by changing "Start" Values in these keys to 0 (Win 7 / Vista ONLY)
HKEY_LOCAL_MACHINE\System\CurrentControlSet\Services\Msahci\Start
HKEY_LOCAL_MACHINE\System\CurrentControlSet\Services\Pciide\Start
HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\services\iaStor
V\Start
If you reinstall windows, all you have to do is be sure the BIOS is set to AHCI before you install, then it will always be in AHCI mode, no matter what port it's installed into.
Yes, windows 7 has directX 11 by default, however some games install specific .dll files or updates to directX while they install. Sounds like your game didn't install this properly or you need to download the latest directX end user runtimes, you can get that here, this will fix the issue
http://www.microsoft.com/download/en/details.aspx?id=35