The top ones are on off/switches, the button ones are phase switches.
The on/off switches just turn the pickups on and off. The phase switches reverse the phase. Reversing phase does nothing for a single pickup, but when you put one pickup "out of phase" with one or more other pickups, you get a different sound. So if you have two pickups on, and you have both their phase switches up, you get one kind of sound. If you flick on of the phase switches down, you will get a different sound, because the two pickups are now out of phase. It doesn't matter which one you flick down - you will get the same sound, because the only thing that matters is that they are out of phase. So if you flicked both switches down, you'd get the same sound as if they were both up, because they are in phase. So it is only the difference in the phase switches that matters, not their position.
If you are looking for a chart of what switch combinations were used in which songs, sorry, no such thing exists. But Brian did use the middle and bridge pickups in phase the majority of the time.