It doesn't matter as long as US citizens enter the US using US passports. I've had DHS do a full search on me, and they found my other passport elsewhere in my bag. After 20-30 minutes of doing a background check, they told me everything was fine and handed both passports back to me.

Keep in mind that for US citizens to have protection abroad (such as embassy services like emergency airlift in the case of riots or government overthrows in the host country), you must enter that country with your US passport.

- Pat