There is no performance difference on a per-drive basis whether it's master or slave. The only thing master/slave settings do is define which drive is considered "first" and which is "second" (drive0 and drive1) for OSes to be able to sort them out. When each drive is active, it is the only active device (IDE channels are only accessible by one device on the cable at any given moment).
You might get slightly better performance overall by having one drive on the Promise controller and one drive on the primary onboard connection, as there will then be no contention for control of the IDE bus. When I said there's no performance difference, I meant in the case of just one drive in the system. Separating drives so that only one device is on a cable at a time helps a little bit, especially if you're transferring files from drive to drive a lot of the time, since both drives can then be active constantly rather than switching back and forth. But otherwise, the performance lost by having two hard drives on the same cable isn't likely to be much.
If you do decide to put one drive on the Promise controller, I'd suggest your OS drive being on the onboard IDE port and a secondary drive on the Promise controller. Your OS drive is likely to get more activity, and you can avoid the PCI bus by using the onboard controller (assuming your chipset's southbridge has the IDE ports directly connected and not passing through the PCI bus, as all or most current chipsets do).