Hi,
The WD6400AAKS is a SATA drive - you don't have to bother about master/slave.
If your motherboard doesn't support SATA II - use a jumper to make the drive run in SATA I mode.
"Opt 1" here:
http://wdc.custhelp.com/cgi-bin/wdc....i=&p_topview=1
Are you going to install XP on the drive?
If so, you need to load a driver (from a floppy) for the motherboard's SATA controller. during setup