As a note to future confused users, here is the procedure for using the Gestalt package, in full, gory detail.
1) Set up the community repository (
full instructions for this step)
2) Once it is set up, go to the Find Updates tab, look for the Gestalt package, select it, and click Download.
It will download, then you will need to click "Start Import", followed by acknowledging that Lone Wolf did not make or review these files. Then click Finished, and load Pathfinder.
3) In the Hero Configuration, turn on the gestalt rules:
I also recommend scrolling to the bottom of the configure screen and setting the XP mode to "No XP Required for Advancement". It just simplifies things a bit, because otherwise Hero Lab will constantly be complaining that you haven't got enough XP to be level 6 when what you've actually got is 2 gestalt levels.
4) Go to the Classes tab and add levels to your PC. Start with the Gestalt class:
The gestalt tab will not appear until you have added a level of Gestalt. Once you have done so, add the two classes you want to mix.
5) Finally, go to the Gestalt tab and select the two classes you added.
There are a couple of steps in the set up that haven't always been explicitly stated before, namely turning it on in the Hero Configuration and adding levels of "Gestalt" to your PC. I hope this helps someone.