As with layouts, you can choose which tables you want to include. You might for example be creating several versions of your app, for contractors, administrators and end users. You only want the admin tables to appear for administrators, but right now you're building for end users. You can select the appropriate tables.
Select the tables you want in your app, and click continue.
Pitfalls
As for selecting layouts, you must include every table that will be visited by any script in your working app. Failure to do so is going to result in unexpected behaviour.