Well,there are some questions I need to know, but maybe I will answer your first. Will you be installing W2k onto a second HDD? If this is the case, which I would say is a wise choice, but not the only option. If your single HDD is large enough then, yes you would install W2k in a separate primary, active partition, but it will be your choice of what file system to use.
First of all create a Extended-Logical FAT or FAT32 partition for your Data Files. This will be a sharing bucket for both Win98SE and W2k. W2k can be installed in a Primary FAT/FAT32/NTFS partitions. If you install W2k in a FAT32 partiton you will not have the best security but you will be able to have access to all partitions with either Win98SE or W2k.
If you use a NTFS partition (recommended) you will have access to all FAT type partitions including where your Data Files are located while booted into W2k. However, while booted into Win98SE you will only have access to your Data Files and any other FAT partitions, but no access to NTFS partition. NTFS partition will be hidden from all other partitions.
If you want the added security that W2k offers, you will first have to create a primary logical partition (2GB limitation)with Partition Magic and make sure that it is ACTIVE. This is where W2k will be installed (Do this only when you are ready to install W2k). During the setup of W2k it will ask you what type of files system to use. For the best security choose the "Convert to NTFS" option. Later you can use Partition Magic to resize this NTFS partition, but make sure you stay within the bootable size limitation of NTFS partiton (8GB limitation).
This will help you decide on the best option for you, but when all else fails we can always read the instruction manuals (smile). I hope this answer your question. Good luck my friend, if I can duel boot so can you. Cheers!
JC-------<*){{{>{~~~~~
Fisher of men