I *think* the motherboard SATA slots decide which is 'master' to boot from.
Therefore SATA1 slot makes that harddrive the master and other slots are slave
(that is if it's set that way in the bios - which might call it something other than SATA1 - it seems to depend on the make of motherboard, so I suggest looking in the BIOS and make a note of the boot order settings)
If you install the new drive swap it with the old one and don't put the old one back in until after you have got all the antivirus and spyware stuff loaded and updated so that you can 'clean' the old drive when you plug it back in as slave.
Others will confirm this or correct me if I have got it wrong.