either one can be the primary one. It's up to you. Here is what i did, i'm using both Win98se and win2k pro. Both has the same file system which is FAT32. I had partition my HD to C: and D: . The C: is where my win98se is installed while the D: is the win2k. With your situation, make another partition using fdisk (in other words, leave alone the win98se), after you had completed it (making the second partition) the file system should be FAT32 as well. If you convert the secondary partition to NTFS, win98se or win2k either one of this OS won't be able to access the C: or D: because both are different file system. In other words, don't use different file systems. Another thing, win98se does not support NTFS...so, in other words, use FAT32 as your file system for both primary and secondary partition.
After you're done partitioning, boot your computer. Make sure your CD-ROM drive is set as the first one to boot, second either your floopy or HD then only network. Insert the win2k CD (sorry, please insert the CD before you boot) and once it gets started, it ask you where you wanna install win2k so you say install it into D: (D: is your secondary partition)...that's about it, and about the dual boot thing, your PC will handle it, which is that after both OS is in your HD, before the computer loads an OS, it will prompt you to choose which OS you want to use. That's about it....anything else? If so, please feel free to e-mail me. Later dude!