Fret not, with Serial ATA being implemented and being the new standard (well, soon enough) the days of jumper settings are coming to a close.
But currently, I use my CD-Rom as master and my Yamaha CDW-F1 as slave. Reason is this, I spent $130 on my burner (best burner on the market) and I don't want to lessen it's life by running my game CD's. The CD-Rom on the other hand is easly replaceable.
So if you have an expencive burner, keep it as slave, and don't use it for everyday things.