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makes no difference unless your batteries are dead and you need a jump start if so you want to charge the passenger side first to jump your truck for giving someone a jump have truck running and use whatever side will reach .
You might check the owners manual. I know mine said to only jump the main battery, think it was drivers side. It had heavier gauge wires on it. Mine was a 97 7.3 though.
The owners manual does not say to use a specific battery for the F-series. But it does for the E-series vans, because the batteries are under the vehicle.
On the F-series, I would use the passenger side battery, because that is the one directly wired to the starter motor.
But I don't think it makes too much difference, and if one were easier to get to in a situation, that's the one I would use. For example, when you can't quite get close enough to the disabled vehicle.