Hi John,
You have just described the technical art of 3d animation ;)
The answer is practice. You will learn how to control all the graph editor spaghetti to make all the controls move the puppet so it does what you want.
At first this will seem daunting because of the amount of curves for a simple character. However, as you gain experience you will learn what you need to pay attention to and when.
You will even start to recognise the patterns in the graph editor and know what the curves should look like in order to make the puppet move in a specific way.
You probably think I'm joking, but I am not.
There's 2 things happening to your brain when taking the animation bootcamp training.
First off, your brain is learning to see (animation), and it is also learning how to control the tool (technical proficiency).
Just take it slow and steady and you will level up.