just a note:
havning the HDD as a Secondary Master, as 'nitestick' mentioned, is Ideal..
..but sometimes the placement of the CD/Optical drive makes it sort impractical if you dont have another bay to put it in. (cause if the Optical drive is Slave, you may need to move it bellow the HDD to get the EIDE cable to fit).
note though: Master or Slave possition for the secondary HDD is fine, you wont notice any perfromance difference between either. so dont stress it.
..incase you dont aready know, once you have it in the comp, you can just go to ->/start/run, type (diskmgmt.msc) hit enter.... then right click on the drive and format it with Default NTFS settings.
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EDIT:
i just noticed on your First post you said you using it on a Barebone setup... witch means that may be the only HDD you have for it right now.... witch means.. if your using that HDD for your Operating system, Yes definalty install it in the Primiary MASTER position.
A little more info:
if you ever add another EIDE HDD to the system.. you wont notice much of a performance diff between Secondary SLAVE/Master, however, you will notice a performance difference between copy operations from 1 HDD to the other, *IF the secondary HDD is on the Primary Slave slot(Same EIDE cable as the First HDD)..
..as long as its ona differetn EIDE cable, it'l be good.