Syncing permissions between a Database project and a database using Visual studio

I have a database project in visual studio (2008) that I am using to keep my database structure in a version control system (Git). I use the data schema compare tool in VS to maintain this database project. The issue that I'm encountering is that I keep losing my permissions for new objects.

So how do I:

1. Capture these permissions using the schema compare tool.
2. Apply these permissions to a server using the schema compare tool.

The easiest method to capture and apply the permissions that I have found is to go into tools -> options -> database tools -> schema compare and uncheck the ignore permissions checkbox. Then run the schema comparision and apply updates.

Note: That this will update every object with permissions in your schema. I have been capturing the permission after I sync my schema changes and then resetting the ignore permissions checkbox