Just to clarify, because I certainly made this a little bit confusing during the beta of 2.6:
(1) Prior to 2.6, the layout was saved with the tournament just as any other part of the tournament, such as the Rounds schedule, the Chips configuration, the Player list. It could also be loaded and saved independently as a template, just like those other parts.
(2) In 2.6 alpha 1, I made the layout a special case, in that it no longer is saved with the tournament. It still can be loaded and saved independently as a template, but it is no longer saved with the tournament, like the rounds schedule, player list, chips configuration, etc, are. This separates the "operation" of a tournament from the "presentation" of the tournament. It also had the side-effect of making tournament save files smaller, which makes them load and save faster. This gives more incentive to use AutoSave, and makes running stats on large numbers of tournaments much more pleasant.
(3) In 2.6 beta 5 I reverted that decision. Now, the *default* behavior is just like it was prior to 2.6. Layouts are saved with the tournament, just like the other parts of the tournament, and may also be loaded and saved independently as a template. However, there is now a preference to allow you to NOT save the layout with the tournament. It's up to you. But the default behavior is just like it was before.