how do you reference server logins from a visual Studio database project?
Right click on references in your SSDT project. Click on Add Database reference. 



Fill out the database reference information here. I bring in the server I am connecting to as a dacpac object, then reference it as a project in the current solution. Seems to work best for me. 

EDIT: I just tested using a database project in the same solution as well and it resolved the references correctly. 


Edit 2: Why this works - Projects within a VS solution do not "talk" to each other, by default. In the real world, servers and databases do "reference" each other. What we are doing here is explicitly making that connection, because the scope of a SSDT project can only be one database. Once you add the SSDT project and sync all the objects, including the security, you need to add that project as a reference in order for it "see" the database objects at the server level.