All your mounted conquistadors will be insanely powerful and are basically your main killing tool. Since the native factions only field infantry, your conquistadors can simply charge anything that isn't a spear unit and suffer scarcely any losses while inflicting huge damage.
Your culverins are also pretty handy, their accuracy has been greatly increased from vanilla so they are pretty effective for sniping the enemy general (or just tearing holes through any enemy unit you don't like the look of).
The basic strategy I found most effective, was a battle line of native mercenaries to pin the enemy and absorb losses, strengthened at key points with dismounted conquistadors/ sword and buckler men, then a crushing conquistador charge to the flanks and rear (almost always possible due to the lack of enemy cavalry). Doubly effective if you've managed to soften up the enemy and pick off the general with culverin fire beforehand.
The only units I wouldn't bother with too much, are pike militia, and musketeers/crossbows. The first are essentially useless since the enemy have no cavalry, while the latter, while in principle pretty powerful, will struggle to make any significant impact due to the sheer numbers of enemy troops you will face.
I found the main problem early on is not the native armies you face as such, so much as the shortage of troops and the large garrisons needed to maintain order. Generally I found it helps to get into the spirit of the conquistadors, and take the attitude that while heavy losses in your Spanish troops (especially your cavalry) are unacceptable, the lives of your native mercenaries are entirely expendable. So long as you can keep the momentum of conquest going, you will be periodically rewarded with new conquistador stacks arriving, as well as being able to upgrade your cities to get your best troops.
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