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The ATA-66 bus is best for your optical drives (they just aren't that fast) while a ATA-100 or better HD will perform best on the ATA-100 bus. That's how it will come from Apple.

As for the second drive, ultimately it's best to have all drives as Master on their own channel. If there is only 1 ATA-100 channel then connect the second drive as slave on ATA-100.
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