Gestalt works in that you combine the two classes into one and level in that single class. So if you multiclass outside of your Gestalted classes, you do not get gestalt. It's why I'm a Martial Artist 2//Fighter 2/Rogue 1 right now.
The campaign... well, we had a little taste with an encounter with Loopers, which seemed like a test battle (as they were just insanely easy to kill). They died before they could float on down. As for the following encounter, it was a naval/sky battle where we were double-teamed. The game kind of ground to a halt due to technical issues around there.
Cleric//Rogue isn't a bad choice at all. We can probably get by with secondary healing (AFB and I can both heal, him with bardic healing and myself with UMD), but it's not like it's reliable in battle (my UMD is a piddling +9... I can up it to +11 with a MW Tool, but it's not like I can get any higher without sacrificing some of my build). I can handle healing at lv 6 with my cohort, however, if you don't want to play a Cleric//Rogue. (Also, flanking buddy!
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If we can fill every slot other than the healer, I'll make my cohort SuperMedicEngineer.
I would lol if someone did a super-classer, namely someone with something like Ranger//Rogue/Swash 1/Ninja 1/Monk 1/Fighter 1 and the respective dual-progression feats. O__O