I made this scenario when I had some free time, so it may be slightly rough on the edges..
Anyway, You start with only a small force (6 Bandereitas, 6 Tercios, 8 Light Cavalry, 4 Ranged Cavalry, 2 Bombards, A Supply Wagon and Pizarro himself) and a handful of Missionaries (Spies). The Idea is that you use these Missionaries to convert (bribe) warriors from the headhunter tribes (don't shy away from allying with a tribe) and destroy those tribes. Your ultimate goal will be to take over Machu Pichu, but beware, it is well defended!!