What is the exact error message that you got? You should be able to link mulitple dbs to the same repository. This is how team members would share changes with each other if they are all developing against their own dedicated db.
On the setup tab, you should use the "Create link..." when linking the first db.
When linking the second db, use the "Link to a db already in source control..." link.
The 2 links are seperate. In the first case, the repository should be empty. In the 2nd case, you need to specifiy a repository folder that contains a RedGate.ssc file. This will set up the links correctly.
If the dbs are 98% identical, we'll try to figure out which version you're at and only show the differences. There are a few known issues around this currently, e.g., if you have an object that is the same, but it's dependency is not, which we're currently working on.