Having two IDs for the iTunes & App Store is simple, and regardless of what ID you have signed into iCloud, you should have the ID that has the majority (if not all) of your purchases signed into iTunes.
I have two IDs as well. My original ID and my @me.com ID. I have made purchases on both. I sign into iTunes with my @me.com Apple account, and when apps that need to be updated that were purchased with my old Apple ID are trying to update, I get a prompt asking me to type in the password to that Apple ID. I also get prompts to type in the password for my husband's Apple ID as I have some apps that he purchased on my device.
So, if you can specifically explain what the issue is, maybe we can find a solution for you. Which ID are you signed into iTunes with? Are you signed into iTunes on both the i-Device and the comptuer with the same ID? If not, why not? What is the particular roadblock you are running into? Provide a clear complete example of the issue.
Cheers,
GB