The master/slave jumper setting for ide drives depends mainly on which connector on the ide cable is used for a particular drive. You can have a single drive by itself on either the end or middle connector. The jumper is set according to which one is used.
For sata drives the port the thinner data cable is plugged into determines whether the drive will be seen as Primary master or slave or Secondary master or slave for that type of hard drive.
The default boot drive or the drive seen as first in the list in the bios setup will be the one the bios searches for boot information in order to see the OS load. If you have Windows on one drive that would be set as the default hard drive. With ide drives or with one present the Windows installer will place boot files and information there even if Windows is installed onto a sata drive. Most will simply unplug an ide drive present to see Windows and all boot information on the selected sata drive and later plug the ide back in to see Windows detect it as a new hardware found.
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