|If you do have a virus, why wouldn't you just remove it rather than swapping out the HDD? And yes, if you connect an infected drive to another system, you risk infecting that system as well. If there is a virus, it has to be removed!|
If these are SATA drives, there is no jumper setting to mess with. If they're both IDE/PATA drives, the main HDD with the OS should be on the primary channel jumpered as master & the other drive should be put on the 2ndary channel - master or slave doesn't matter. If there is no 2ndary channel, the 2nd HDD would obviously need to be jumpered as slave.
If you have a mix of SATA & IDE/PATA drives, we need to know which is which.