These are serious questions that deserve candid answers:
1. The native women in the missions worked quite hard, primarily at cooking, cleaning, making clothes etc. The hours were long but consistent with contemporary practice. The young women were provided special housing to protect them and provide a special environment.
2. There was extensive courting of the native women by the soldiers stationed at each mission (4-5) and presidios, and many of the soldiers married native American women, typically in unions that survived. While you are correct to call the soldiers Spanish, in that Spain controlled this territory, most of the soldiers were not from Spain but rather New Spain (today's Mexico), often of mixed blood.
3. Most of the women made an effort to keep their children in touch with their heritage. In the early days they frequently made visits back to their village. However the children were taught Spanish and quickly assimilated into the new environment, not unlike second and third generations today. The Indian beliefs and practices however, had a major impact on the food eaten and even the liturgy.
4. The neophytes (converted Indians) lived in special housing near the main quadrangle which contained the church, padre's quarters, workshops etc. These were one story apartment like dwellings. One has been carefully preserved and restored You can see this at the Santa Cruz Mission State Park (adjacent to but not part of the mission).
5. The soldiers were often cruel, particularly during the difficult transition years before and during the transition from Spain to Mexico, when they were typically underpaid or not paid at all for long periods, and when there were Indian uprisings. There were jails and flogging was used for serious crimes.
6. There did not seem to be as widespread abuse of alcohol as found on the Indian Reservations in 19th century, in part because these were pretty well managed, self-contained communities.
In general the majority of the native Americans made the transition into the mission community successfully but some percentage (10-15% we estimate) did not and became "run-aways." Over time the neophytes were totally assimilated and many came to cherish this life and found it difficult to leave when the missions were secularized