IRQ problems with a SCSI card? Most probably, absolutely, not. Basically noone actually has IRQ problems, that's a myth. It's just that every unsolvable mystery is declared an IRQ problem. Forget that idea.
But if you believe in that BS, anyway, let me say again that onboard devices sit on the same PCI bus and set of interrupt lines as the cards in the slots do.
For the 239847619723rd time: PCI devices MUST, by definition and standard, be able to share IRQ. So do AGP devices. This is not your problem, even if three thousand internet "experts" suggest so. It's all either buggy drivers, or in case of SCSI, improper cabling and device setup.
Vent over, back to the topic. LSI's or Tekram's SCSI controller cards (which also use LSI chips, firmware and drivers) happily accept HDDs that have been on Adaptec controllers before. Use those.