Right-Click on your project, and select Properties.
Java Build Path -> Source -> Link Source
Click the Browse Button and select the external folder where your sources are.
Enter a folder name, or leave the default name if it suits you. This name will be used in your Eclipse project.
Leave Ignore nesting conflicts on, and click next.
Here, you can add "*.bak" in Exclusion Patterns, but I don't think it's needed, because bak file won't be compiled anyway.
Click Finish.