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.
Thanks for the help. I was able to save with both methods.
Martin is correct. The trick is when you "saved" it earlier, you were saving it to the "clipbase," which is basically a temporary database that is open by default when you start the program. It is much like the "clipboard" idea where you can copy/paste data to and from in most operating systems. To actually save it to some place permanent, you need to create a new or open an existing database and make sure it is active (the database switcher window will help switch between open databases -- you will see the clipbase there). As Martin said, you can also just export it to a pgn file. As you work with larger numbers of games, you will find the database method far superior, but for single games or small numbers of games, pgn is great, too.
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