You shouldn't be setting them both to slaves - you might be able to turn off the warning somewhere in the BIOS but this isn't really getting to the heart of the problem and even if it works it'll only be a bodge
When the disk wasn't showing up previously, you say you've checked the jumpers but have you also checked the drives' positions in the IDE cable? The master should be on the end and the slave should be in the middle. Also, have you got two IDE channels available or just the one? If it's two, then can you plug the two drives as masters into separate channels rather than in the same one?
One thing that I'm confused by is this:
...since any other way it would choose the secondary IDE HDD as master over the primary SATA2
What do you mean by this? SATA doesn't have the concept of master or slave drives, this is an IDE thing. Do you mean the drive wasn't detected at all, or something else?
If it's a case of you set your drives up correctly and windows put your IDE hard drive as C:\ and your SATA as D:\ or something similar, then shout - that can be fixed pretty easily.