Yes, that's very common. Our IT group has the same type of situation. The bug tracker software tracks very specific items and their personal systems track everything else. Or, just duplicate it. I almost always err on the side of my system taking the load of tracking what I am committed to complete, even if it's tracked somewhere else as well.
It's actually very similar to a CRM (Customer Relationship) system. Same idea--just different software. Check out this article on GTD Times for idea on how one of our coaches recommends managing that.
Hope this helps,