Missions were manned by franciscan monks attempting

Missions were manned by Franciscan Monks attempting to Christianize the Indians,
indoctrinate them into the Spanish ways, (making them loyal to the King of Spain), and
to help hold the territory against intruders. The mission grounds usually included a
chapel and living quarters for the holy men and whatever friendly Indians wanted to live
there. Sometimes a protective wall, workrooms, and storerooms completed the facility.
Fields and pastures were maintained beyond the walls. Towns were rigidly laid out with
the streets perpendicular according to the 4 cardinal directions. The east side was
reserved for the church; the west side they designated for the government. The Friars
instructed the Indians in Christianity, employing a rigid religious routine, enforced by
corporal punishment. Exploitation for labor was rampant. Few Indians thought such
tactics tolerable, although some Indians sought new allies or at least safe refuge in the
missions from the fiercer tribes. Unfortunately, the afore-mentioned disease took a
terrible toll on the Indians who regularly interacted with the missionaries. Some Indians
believed that it was the baptism of Holy Water that was generating the deaths.
In many cases, the various Indian
tribes were such sworn enemies that
separate missions had to be
established for the various tribes in
order to avoid bloodshed.
If a mission was particularly successful,
sometimes settlers from Mexico would
come and join, creating ranchos
stocked with cattle and even villas , with
shops and artisans. At such a point the
mission would convert into a local
parish, and the missionaries would
move on. The Spanish crown was usually generous in granting land to those who would
brave this frontier. Unfortunately, success usually attracted the attention of the more
aggressive Indians who would be drawn to the mission for the opportunity to plunder.
The Spanish also built presidios (small forts) manned by a handful of soldiers to protect
the mission. These forts were typically under-manned and under-equipped to seriously
defend a territory from the warrior tribes. One presidio was found to have only 2 guns
and 2 shields for its 60-man contingent and suffered further from an inadequate number
of horses. The chain of command was tightly maintained, and few officials were inclined
to do anything without approval from above. The decision-making process stretched
across the Atlantic to Spain. The communication and supply process often took years.

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The idea of the "sword and cross" working together was a good example of the unity
of Church and state in Spain. The Crown would oversee and promote the spread of
Catholicism and maintain the Church. In return, the Church would endorse the aims of
the State and tolerate political intervention in ecclesiastical affairs. Remember, such
roots were well-established since the Moslem invasion.