Partitioning my HD

Once you have the partition space to load the OS
Insert the W2K Pro disk in CD-ROM,choose the clean install option
Setup will start to install and you will be given the option of what type of file system you will prefer to use,if you choose the NTFS file system ,keep in mind that Windows 98 will not be able to read the NTFS partition,but you can read a fat 32 partition,so if security is a concern you will use select the NTFS partition.
Using a third party partitioning utility you will be able to select the file system format when you partition the drive.

In my opinion the best way ist to use a bootmanager.
I've prepared some harddisks in that way.
Look for the tool GDISK first. It replaces for example fdisk. With gdisk you can create partition at commandline. The best to do it before installing OSes. Look for the manual.
For example I would install 2 primary partition and one extended for Data (FAT).
Then take the tool Xfdisk. Xfdisk allows you to create a bootmanager, and inserting the 2 primary partition as boot menu. the advantage is, that the partition you don't boot is hidden.
All our testclients have for example 3 primary one extanded.
First small W98 for using ghost
Second NT4
Third W2k

Extended for the ghost images

Good luck from germany