I assume you want to add w2k advanced server in addition to 98se. I did this about a month ago. I had absolutely no problems doing it. Simply run the install cd and tell it you want to add w2k advanced in addition, not as an upgrade. When it asks you, you want to keep fat32, not change to ntfs. After the installation was complete, w2k advanced was my default os, but you can easily change that if you wish. You will have to reinstall your programs for w2k though. I dont guarantee everything will go without a hitch for you (just my disclaimer so I don't get yelled at later) but it went fairly straight forward for me. No Problems.
ps. you don't need to partition yourself. Everything is taken care of during setup.