Gestalt characters aren't as much "better" as it looks like they might be on the surface. They've got the best of the abilities from two classes, but that means they don't get any more skill points or feats than the best single class they selected - and they have to divide those resources, plus their wealth, across the demands of both their roles. Frequently, gestalt characters end up being good at one of their classes, and okay at the other, because of that division of resources.
When we ran with gestalt characters, we had only 2 PCs, and they needed to be good at both roles, so we increased the skill points and accelerated the feat progression. I wouldn't necessarily do that if you have more than 2 PCs, however.
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Gestalt PCs can typically take on challenges about 2 CRs higher* than their actual level. This means you'll be throwing tougher challenges at the PCs. I strongly recommend that you subtract 2* from the CR of each creature before determining the XP values. Otherwise, you'll really accelerate the leveling up, and the game could feel like it's getting out of control. And you want to subtract from the actual CR, rather than count the PCs as 2* levels higher, because again, you'd be increasing the XPs too much if you do it the other way.
You'll also want to make a decision about treasure. Are you going to let them get treasure equivalent to the CRs they deal with (which will give them the wealth of PCs 2 levels higher, and will result in the need to increase CRs of opponents still more), or reduce the treasures that NPCs and monsters have by about 2 CRs* (which means NPCs will have very little wealth compared to their levels)? You'll probably end up mixing the two methods, and you'll probably want to keep track of where the PCs actually are, wealth-wise.
*The actual amount of extra challenge can vary - whatever amount you feel like you're increasing the CRs of reasonable challenges by, that's the amount by which to recude those CRs before calculating XPs.