no, things will work just fine.
when using only the ATA100 drive, the bus will transfer at ATA100 speeds, when using the ATA66 drive the buss will transfer at ATA66 speeds.
you can read more about stuff in this FAQ:
[url=http://www.cdrlabs.com/phpBB/viewtopic.php?t=3032]What are DMA and UDMA ?
there are a few links there to pages that contain plenty of info about all this stuff.
One Ring to rule them all, One Ring to find them,
One Ring to bring them all and in the darkness bind them
In the land of Mordor, where the Shadows lie
M.C. Escher - Reptilien