Proteins - figured out?

I might have figured out the protein debaggle (is that even a word?) that's been circling in my head the past 4 days.

One can eat a protein-rich diet. Excess protein is broken down and converted to amino acids (the body does not 'store' protein, it merely uses and recycles it). Amino acids (an enzyme) builds up to what the body can use. In the end, anything the body doesn't use is broken apart and converted and stored as fat (other excesses are lost in urine). Fat is stored and used as energy.

Then we have the thought... carbohydrates are our primary source of energy. When the body has used up all its carb-based energy, it turns to protein-based energy. Proteins are the last source we want our body to use, because then it interfers with things like muscle (it will essentially eat away any present muscle) and we waste away to 'nothing' (worst-case scenario).

My understanding is halted trying to understand and connect the two. In my studying, I find I understand things as I'm reading them individually, but I need to put into practice more involving one with the other, creating the bigger picture.