Saving a layout saves everything you can modify on the Layout tab. It doesn't save Rules.
Here's a quick overview that might make this more clear:
- Anything labeled a "preference" is an application parameter. These settings determine how the application behaves and are persisted automatically by the application. The currency symbol to use when displaying money, whether or not to run in "full-screen mode", etc.
- Everything else is part of a tournament. If you save a tournament, essentially everything else (everything besides "preferences") gets saved with the tournament. The tournament is divided into logical sections (rounds, prizes, players, etc), and each of those can be loaded/saved independently as templates. But they are all saved with the tournament as well.
- The Layout is the presentation of your tournament to your players, and is the exception to the previous item. Because the layout isn't part of the logical make-up of a tournament, it may be saved with the tournament or independently from your tournament, as determined by your preferences. The layout draws information from your tournament to display to your players, by way of <tokens>. The <rules> token, for example, displays to your players the value of the rules token defined on the Rules tab.