I'm not 100% sure on Linux but you should have a couple of options.
First is to create a database. When you do that, you can enter all your games and comments into it and load it each time you launch the application. You should be prompted where to save the DB when creating it.
The other option is to export the current game(s) to a PGN file. I believe that is in the Tools menu and you will be able to specify a location in that process.
I recently downloaded SCID to analyze games. I would like to save manually entered games and comments, but for some reason I'm not seeing how to do it. The save box comes up, I enter info, click save, and it goes somewhere, but where?
A little help please