If you're not driving the car for 2 months or more, then disconnect the battery. The computer, clocks, etc, will continue to draw a small current, and if you leave the battery connected you may get a dead battery when you come back.

Nothing wrong with resetting the computer of the car. Sure it may take a few days for it to "learn" your driving habits and set the optimum operating parameters, but there's nothing it will do to harm the car itself. More likely it'll run rich and use a little more gas (and probably not pass emission test). After a few days, you're fine.

And yes, you'll need to reset the clock, and there's any alarm or security system on the car, you'll need to punch in the correct code. So, know what they are beforehand.