well i bought a new guitar, and it has these pickups that you can adjust their height. by screws...well it only has 2 pickups, and and each pickup has 12 magnets. or whatever they are. i dont know what their called. but anyways. one is at the top by the fingerbpard and the other one is at the bottom. which lvls should they be at?

is the first one suppost to be lower, and the bottom one higher? or vice versa. or should they be even

it also lets me lvl the pickup where i can get it closer to the thicker strings or higher to the smaller strings. Anyone have suggestions?

cuz im not sure.

does that affect my trebal/rhythem switch?

my guitar is an epiphone les paul special 2
Adjust to to how you like. If they are level the bass and treble should be even. If one is higher than the others you will get a more stronger sound from which ever side is higher. And no it will not effect your switch.
Closer to the strings means it'll be louder, but also have less sustain (meaning your notes will fade out very quickly)