Sorry about the confusion, as there's no specific system you were asking about.
VirtualRain's correct, as there is a difference between the '08 and '09's, and should have mentioned it in the earlier post. Both have 6 SATA ports, but the lack of the PATA ports on the '09 means one is used by the stock optical drive, assuming the second wasn't ordered.
So you've got a couple of choices.
1 a. Get an internal SATA card. Syba makes a couple that are Mac compatible, and fairly inexpensive as well. ~$20USD or so, last I looked. You'd need a long enough SATA cable to go from the card to the open optical bay. Power would be a little more difficult, as the connector used is a backplane part (power + data in one connector). If you're comfortable doing it, you could tie into the power cabling that goes into the connector with a SATA power cable. You might want to use a DMM to make sure you get the correct wires connected. Wiki has the pin-outs for the power connectors BTW.
1 b. Again, use the SATA card, but use some hacked 3rd party cables (power). Use one of
these (Backplane exention cables). Get a standard
Molex to SATA power connector as well. Cut the Molex end off the power cable. Tie the power wires with the corresponding color to the backplane cable's power leads. Crimp connections or solder + heat shrink would work rather well, and make routing/tucking easier than wire nuts. Much easier than directly hacking the original wiring in the MP as well. (Better if it ever had to go back for warranty repair or replacement). It's downside is, you now have more of a cable rat's nest to deal with. Either method would be less expensive than option #2 though.
2. Move the optical drive into an external enclosure (USB/FW800). This would cost more, but might be the easiest way to go.
A third option exists, via one of the HDD bays. It's a particular sled that uses a Port Multiplier chip, which allows 2 drives to use a single port. But there is a speed penalty for doing this. It would be noticed with SSD's, particularly those capable of ~250MB/s. Absolutely the case if you plan to do RAID 0 with them.
I hope this isn't too confusing.