If your going to use the SATA Drive As Storage, and Not put your OS on it, Then this Is what I would do.
While computer is off attach the Molex connector to the SATA Drive then Attach the SATA Data cable to the Drive, turn on computer, allow it to boot up and get to desk top, then Plug in the other end of the SATA Cable to the motherboard, you can then Partition it and Format it through disk Managment. After which there should be no booting Problems, SATA Drives are always Master, but in this case your Computer will boot off the IDE Drive since it has always done so.
In fact, you could attach it even while the computer is off, It should boot off the IDE Drive reguardless of what SATA Drive is attached, Unless the SATA Drive has an OS on it.