It doesn't matter, your boot loader for your flavor of linux should recognize NTFS or FAT32. Your choice of FAT32 or NTFS for your windows operating system depends on your purpose, supposely NTFS is faster, but i can't really tell difference, and also it you need to access your drive thru DOS, you sh#t up the creek if used all NTFS. Mandrake 8.1 has a good bootloader.
If you're really new to this and worried, just get removable hard drive racks and buy cheapie hard drive in the For/Sale forum. Just swap drive for you purposes. We use this technique a lot for software quality assurance for on the fly testing.
Oh, I want to apologize to everybody, i put Andy in bad mood, he realizes now that I have better taste in music and women
