If these are for the current database, your best bet is to import the project, then just replace "MyDBName.dbo." with "dbo.". If you're trying to reference other databases, you should probably use SQLPackage to extract a dacpac for those, then add database references for them. When adding the database reference, do not choose the option to treat these as a variable unless the names of those databases change from environment to environment. E.g., if you reference MyDB1.dbo.Table1 in your project and "MyDB1" is always the name of that database, you should not try to use a DB Variable.
I've written about this on my blog. Maybe that will give some better examples.
http://schottsql.blogspot.com/2012/10/ssdt-external-database-references.html
and
http://schottsql.blogspot.com/2013/01/ssdt-publishing-and-referenced-databases.html