Adding the Sonnet card should not affect your ability to boot from CDs.   Leave the optical drive connected to the built-in ATA bus.  There's no reason to put it on the ATA-100/133 bus.  

If the Sonnet cards have proper firmware, even if you move the optical drive to them, it should still boot properly.   I'm not that familiar with the Sonnet cards, though.   Optical drives work on the VST UltraTek-66 and on the Acard cards, that I know of, perhaps others as well.