Windows will overwrite the MBR on the hard drive if you install 9X/ME after NT/2K, but then once it does that, you can use FDISK /MBR to restore the old MBR, and then manually edit boot.ini to reflect the new partitioning scheme. To boot Win9X, just add another option to the boot order such as:
"Windows 98"=C:\
You don't have to do the entire ARC path like NT requires (eg. multi(0)disk(0)partition(1)...) to run Windows.
Now...as to which one saves more time, that's your call. If you think it's easier to keep Win2K installed and simply hunt for every occurrence of "C:" in the registry and change it all to your new drive letter, that's your deal. It took me about fifteen minutes using copy-paste-keyboard shortcuts to fix the entire registry in safe mode...But it worked.
Yeah, I think that WinME recognizes different pre-existing Windows OSes, and so it doesn't interfere with anything, but Windows didn't do that before. But as it was said elsewhere, I'm finding little reason to use 98 anymore. The only reason I keep that partition is so that I can easily play a game on it, and then scrub the partition and get a clean Windows again. This way, any game I test will have the same clean slate. But Quake 2 runs just the same in Win2K as it does in Win98...

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"And knowing is half the battle!"