Bootloader: When your computer starts up the BIOS (basic input output system) does a bunch of checks to see if everything's working, and then it goes to your first harddrive (typically your master HDD of the first IDE channel). This is what happens when you see all that text flashing across your screen just after you've switched on your computer. The BIOS then searches for the boot sector, a very small "partition" in the beginning of your hdd. And loads the program it finds there. (This is what happens after the text goes away) That program is called a bootloader... It knows where all your operating systems are stored, and knows how to make them start.
Windows' bootloader can only load windows OS's (operating systems), but linux can load your windows as well...
So in effect when you install linux, you shouldn't need to worry about which hdd is master or slave, your bootloader will keep track of that and give you the option to load windows or linux.
It might however be better to just take out the windows drive first, and make sure everything's working, you might have to install linux over again, but this way you know things won't go wrong and mess up your windows...
I agree with muddywaters. If both knoppix and Ubuntu don't work there might be something else... I'd try that first...
You might want to do it like this:
1. Take out windows drive so you know you it's safe
2. Put in your other drive, doesn't matter if it's master or slave
3. Run knoppix live cd the way muddywater suggested (this disables some functions that might be the reason for things going wrong)
4. If knoppix works, try out ubuntu or other live CD's and just get a feel for the different distributions of linux.
5. Choose your favourite one and install that.
If you want to download SuSE in the meantime (it's quite big compared to Ubuntu) there's two ways:
1. 5 cd's, the 6th is optional, but is nice to have, contains flash, java, acrobat reader and other non opensource programs you'd otherwise have to download.
2. a DVD
If you want to have a live (no install) version there's a dvd:
These links can be found on: