Can't tell you what setting you should use but will give you my configuration as an example...
Just today I took a formatted & partitioned drive out of one case and put it in a new MiniStack enclosure. The directions said explicately to set the jumper/s for Master. I'd been using it in another case set as Cable Select. My computer, an MDD G4, uses internal drive settings on Cable Select. So, even tho' I thought about it, I decided to just leave it on CS and hoped all would be right with it.
It was... as soon as it was hooked up and turned on in FW mode, the partitions appeared on the desktop and it was good to go. Love CS because it takes the guesswork out of it.
This probably didn't help but good luck finding out what you should use.
Laurel