how will gutsy deal with synaptic and CNR at once?

This is something for developers to think of.. Im not really a developer and had no idea where to put it. How will Gutsy deal with both systems at once? Will installing from CNR still allow you to receive updates automatically like with synaptic? What if you install from both, etc.. I think there might be issues, like being able to install the same application from both, the user should be warned they already have the program for example. Also when you want to remove a program and you forget where you installed it from, I think there should be some kind of loose integration. Thats what I think but I'm no developer or computer expert.