I'm brand new to Linux too, dealing with same thing. I use Windows XP Pro on my slave IDE HD; ME on my primary. I used to have 2 XPs, one on slave, one on master; plus the ME. For Windows, you can change IDE pref at the BIOS in 5 or 10 seconds on boot-up, choosing either IDE Drive (0) or (1), which remains default forever until you change it again. An even sweeter method is using US-BOOT's free boot manager with its slick menu; you power up with a floppy and make your choice between IDE drives in 1-2 seconds.
--Linux seems less agreeable, but that must be because I'm brand new. I'm changing to Linux because I've heard it does everything better. So far, it's balked at my wanting more than one partition to be bootable. Actually all 6 of my partitions on my 2 IDE HDDs are primary bootable. On Linux Morphix I had to choose between XP and Linux; I suppose because they're so different. (That was no problem between XP and ME, which are also different O/Ss on different kernals.) Anyway, I did create a Linux partition yesterday, but then the Morphix installer died, so I'm working on that today. I notice that XP Pro agreeably recognizes the Linux partition in terms of its existence, size, and Linux identity.
--That's not much help to you, but maybe it gives you some background, plus encouragement in knowing you're not alone! Best of luck. :-)