BootMagic will automatically set any "conflicting" partitions to be hidden when it switches
between OSes. You can change that option in its settings.
The Windows (98 and ME) versions won't share a boot record, BM controls which boot
record gets control as is switches between partitions, hiding the ones that are not needed.
Also, Windows 98 and ME don't have to be installed on C:, they just need a C: primary
partition to boot from AFAIR.
(if you know the tricks to get them set up that way, usually its easier to just have different
partitions for each)