Win98SE & 2000 on same HHD

I just installed Win2000Pro onto a partition (25GB) on my main HDD (120GB) that
also has Win98SE on it.
Win98SE is on the C:\drive and Win2000Pro is on the i drive.
I formatted the Win2000Pro partition to the NTFS format while 98 and the others
are still FAT32.
Was that a mistake? Seems that Win98SE cannot recognize the new system but 2000
can see and access the 98 drives. I have no real problem with that, so far.

Two more questions:

I installed another copy on my anti-virus on the new 2000Pro and I also
installed another copy of AdAware and SpywareBlaster on the new 2000 partition.
Is it necessary or advisable to have two copies of the same antivirus on one HDD
containing both SE and Win2000Pro system?
Do I also have to install another ZAPro on the new system? ( believe I do )
Would there have been a better way to do it while utilizing only one HDD?

Thanks,
Buffalo

PS:I can start over with the Win2000 system since I don't have that much on it
yet (the updates did take quite awhile though).