I am not clear as to what your concern is but here goes. This applies to IDE controlers not SATA. Most all drives can be set for Master, Slave or Cable Select. This just is an indication of their position on the cable with Master at the end and Slave in the second position. If you are using 80 pin cables you can use Cable Select and the system should (in theory) identify the drive automatically. These settings are achieved with a jumper on the back of the drive.
Other than a few anomalies, any drive should work in any position. Some Zip drives were an exception. Most people try to keep their hard drives on one cable and their optical drives on another. I have noticed copying is faster when source and destination are on different cables. In addition to the two IDE controlers on the motherboard, you can get a controler that will plug into a PCI slot and give you the ability to add additional drives beyond the usual 4, but these can be flakey if you hibernate a lot. Also some older mother boards have trouble booting from a controler off the board.
You should be able to install and set the jumpers and leave it. I have not had to redo this unless I added something new. Hope this helps.