If Auto-Feint is off, then to perform skill moves you must know and input the correct left/right stick combinations for each skill move.
If Auto-Feint is on, then the game will decide for you which skill move to use and you don't need to be exact with your inputs.
Personally I've gone back n forth. I'd like to keep Auto-Feint off because it gives you more control and rewards you for inputing the right move at the right time, and if you have it on you never can be 100% sure which skill move the game will do.
The problem I find is that the skill moves in PES have very unintuitive controls and I find some of them nearly impossible to recreate in the game. So right now I'm back to having Auto-Feint on.
My recommendation would be to master the basics of the game and only once you're comfortable on the higher difficulty settings, then maybe start playing with auto-feints turned off. To each's own but I find this way it's less overwhelming because trust me, learning the different skill controls ain't easy.