That's easy to confuse, I just happened to have done lots of research for my MacPro.
MacPro , early 2008 and before : 2 empty SATA ports on the motherboard, can be used for extra internal harddrives, eSATA brackets to connect ecternal eSATA enclosures (one per), etc. . Need to lead cables from Mobo to device .
Optical drive : IDE , unused power connector in optical bay (needs adapter).
MacPro , late 2008 - today : One unused SATA connector in lower optical bay, connects straight to any SATA device (one); optical drive : SATA .