study up a little on bootloaders
there are several options
serial/sata drives have no master/slave jumpers or cable placement to figure out
you could even use bios to set the new sata drive to boot temporarily while you install vista then just change it back to boot to linux, and if you have the option just use a keystroke command to boot to the vista hard drive
personally I would use xp as the alternative to linux, linux won't do a lot of stuff, vista has the same problem, xp is probably the best all round OS.