Note that I haven't used every motherboard, but every motherboard I have used has the SATA controller and the usualy primary and secondary paired IDE controllers completely separate.
Some of the motherboards have SATA RAID controllers that have both IDE and SATA connectors. I have no knowledge how that works?
Any ways, they still have a primary and secondary IDE controller pair that is separate.
Just attach your IDE drive to the primary, or secondary, IDE controller as would normally be appropriate. (I.E. If no other drive is attached, then attach it as a Master, if another drive is there attach it as a slave, or make it a Master and the other one a slave.)
In the BIOS you generally have to specify what controller is going to be the primary boot controller. (This is different for each BIOS.) Often selecting the boot order alone is enough, sometimes there are other options that must be set as well.
The entire process should not be a problem.