Ric,
By default ProjectGen creates add-ins which use a reference to the proxy.dll in the GAC. As long as you are reinstalling the latest copy of the proxy in the GAC and don't change your add-ins to use a local copy, your add-ins will see the changes. If you change something in the proxy like a scope, parameter type, or return type that an add-in was already using, the add-in will need to be recompiled.
In the ShapeAppSamples the proxy is added to the GAC in a post build event. For instructions on how to set up your host this way, please see Moving and Organizing DLL’s to Make VSTA Integration Easier. Part IV- Keeping the current Proxy in the GAC. Updated for VSTA v 2.
The registry hive does not need to be edited for changes to the proxy. The only time the registries need to be changed is if you add an In-Process Host or want to change a setting you specified prior to running vsta /setup.
Hope this helps!
-Melody