I have a tri-boot (98/NT/SuSE Linux) & several duallys (98/Mandrake, 98se/Red Hat, win2k pro/win2k advanced server). What you're describing is a bit tricky but do-able.
First - since 98 is not that sophisticated, you'll need enough space to install it (system files) on C:... so you might consider making C: bigger. Also the installer needs enough space to expand the compressed cab files (those temp files will be deleted afterwards though). 98 also needs contiguous partitions to be able to access them, so the FAT16 C:, FAT32 D: is cool. NT can install to a different partition (the NTFS one I assume), but won't be able to do anything with the D:. It should be able to read C: though (and you could transfer files between the two OSs that way).
Also, make sure you install 98 *first*. When you install NT later, it will modify the mbr (master boot record) on C: and create a boot.ini file that will allow you to choose the OS. The boot.ini file will be located in \%systemroot%\ (or what you would define as E:\ - note that that drive letter might change depending on what drive letter your CDROM is assigned). Boot.ini is read-only by default, so if you ever need to modify it (ie., to change the default name that shows up at boot time for Windows 95/98 from the word "Windows" to "Windows 98", you'd need to make it writeable.
Anyway... try this:
C: - 500MB (FAT16)
D: - 4GB (FAT32)
E: (or whatever) - 1.5GB (NTFS)
I may come back and edit this if I find it confuses me!
