Hi Jinskee,
You should have no problems, Tim clearly labels each pair of pick up wires - and even if the chaps at the shop are drunk at the time, you will be able to notice if the toggle switch on your guitar gives you the opposite effect when selected ( i.e. more mellow in the treble position ). As to pickup heights, Tim recommends between 2-3mm gap from the underside of the string to pole piece, with the strings held down at the last fret. Then adjust to taste. I tend to like nearer 3mm + for sweetness, some like 2mm for real 'bite'.
Bear in mind that on a Les Paul, the bridge pickup will look a lot higher up than the neck even with the above gaps are set about equal.
Enjoy ! :D