Your reasoning is faulty. It is true that in electro-STATICS (ie when there is no movement of electric charges) the electric field inside a conductor is zero. But this is not the case for electro-DYNAMICS (ie when charges are in motion), eg when there is an electrical current flowing.
It is also true that, for alternating currents, the current becomes more concentrated near the surface of the conductor as the frequency increases (the Skin Effect). However, when the frequency is low or zero (eg direct current, DC), the current flows throughout the cross-section of the conducting wire, not only near the surface.
I think you are confusing these two different facts. The first one (no electrostatic field inside a conductor) does not explain or cause the second (alternating current concentrated near surface of conductor).
I don't understand what argument you are making about the use of Ampere's Law and what you find contradictory.