The Spanish had rules for almost EVERYTHING and EVERYBODY . They had what we would call today big manuals describing how a mission should be founded, how the mission should be built and how it should operate.
The padres were governed by the rules of their Franciscan order (for example they couldn't own anything) and they had to sign a contract with the government to agree to stay in California for ten years.
The soldiers, like the soldiers in every army had rules of governing their behavior, dress and relations with the natives.
You didn't mention the neophytes but their lives were very regimented too.