You would have been better off if you has started in Site Admin by creating a new project as a copy of the one from which you copied the database schema. If that is still an option, I would recommend you do that now instead of trying to connect to your manually created project schema.
If that isn't an option, then my suggestion is that you use Site Admin to create a new, empty project. Then use Site Admin to Remove (not delete) the project. Then go to the file system where you QC repository is stored. Find the dbid.xml file for the new empty project. Edit that file so that it references the project database that you manually created. Then go into Site Admin and import that new, no-longer-empty project.
If that isn't an option, then my suggestion is that you use Site Admin to create a new, empty project. Then use Site Admin to Remove (not delete) the project. Then go to the file system where you QC repository is stored. Find the dbid.xml file for the new empty project. Edit that file so that it references the project database that you manually created. Then go into Site Admin and import that new, no-longer-empty project.