Having just finished a leather water bottle, I can give two useful tips on this, but do search for Bardster's info on water bottles, as they are excellent!
Firstly, make sure the leather is warm before applying beeswax, this helps it soak in better, as the wax doesn't cool as quickly and the leather is more receptive to absorbing it.
Secondly, if you get too much wax on any part, it can be easily removed by hairdrying and rubbing and smoothing with a (lint-free) cloth.
Let us see pictures of it when its finished!