If you use –prefix=/usr in the configure then it should overwrite most stuff. Thats how I did it. I also first installed it from the deb package and then later compiled over it.
Please note that most likely some of the flac, ogg, avahi and so dev packets will be missing. You need to install em first with the packet management system. But if you forget then the configure will complain and remind you, provided you used the proper –enable-xxx flags to include the stuff you want in.