Unfortunately there's no way to automate this. As each DB would need to link to it's own folder within your repository, there's no way for SQL Source Control to know where or what these would be.
Is it important that you link *all* of the databases from the outset?
In any case, this is something that's been asked for previously. We are already looking into ways of improving the initial configuration so I'd ask you to vote for the feature request here
and add any comments you may have.