The first thing you need to do before baking out everything is getting a solid lowpoly mesh with good UV and no errors. Creating a sloppy lowpoly can cause significant problems later on as you need to redo all the bakes all over. In order to make the baking easier it's more safe to make the bigger changes to the highpoly and not just the lowpoly.
The bakes I use are a lighting map, AO, vertex color, normal map, gradient map, concavity, convexity and overall AO(since I bake my
parts separately). I also bake an SSS map for the skin but the results have varied a bit over the range of characters I've made so they usually
require a bit of tweaking as opposed to the other ones.