The BIOS section of the manual doesn't put any restrictions on the SATA ports. You do need to make sure the SATA controller is Enabled in the BIOS and set to IDE mode.
The BIOS menu doesn't give details about what the options are in Boot Priority, but the impression given is that any hard drive attached can be chosen as the Boot drive. See page 4-39. Indeed, you can select which Optical (CD/DVD) drive would boot first also.
Normally, a CD or DVD drive can be any drive on any connector. It's typical to put the CD as a Slave on and IDE connection but rarely required. Even though some systems refer to the 2nd or 4th, etc SATA connectors as Slaves, there is really no such thing.
Generally, in a system like yours with two pairs of IDE connections and 2 SATA connections, the ports are called as follows:
1st Master -- 1st IDE drive on IDE header 1
1st Slave -- 2nd IDE drive on IDE header 1
2nd Master -- 1st IDE drive on IDE header 2
2nd Slave -- 2nd IDE drive on IDE header 2
3rd Master -- 1st SATA port
3rd Slave -- 2nd SATA port
So, you should be able to put the SATA drives, HDD or DVD, on either port connector, making either port 1st in boot priority.