| Bobson |
There's nothing about gestalt which is incompatible with Pathfinder, but like any non-Paizo product, you're more-or-less on your own for figuring out how to integrate it into your game, and you should work with your GM to figure it out.
The way I've generally understood it, you need to consider each combination of classes as one "class" that happens to get the best abilities from each of the two regular classes. Thus, you could take 10 levels of Fighter/Rogue as one class, and 10 levels of Fighter/Wizard as your next one. For the first 10, you'd accumulate 10 levels of everything that F/R gives you (Full BAB, Good Fort and Reflex, Sneak attack, feats...), and then for the next 10 you'd add the benefits of a F/W (Full BAB, Good Fort and Will, Spellcasting, feats...). It's just like multiclassing Fighter 10 / Wizard 10, except you get more with each level.