first of all, I´d rather learn rigging without any tools first. this way you get to know the major needs and problems within the process of enveloping.

take the LRA for example. you can´t zero it when having input connections on your joint chain. you have to zero it first and orient the joints fitting your needs then. I use X pointing down the chain with +Z as the bending axis. when the skeleton is set up you might create a bind pose. as soon as you have some kind of input connects like a skin or set driven keys, you end in a mess if you didn´t create a clean joint hierarchy first. good tool I use is from paul thuriot - the templateSkeletonLE.mel but i find it important to understand first what scripts do for you later.