Surnames in the 1600s and early 1700

I have recently been looking at a lot of the matrimonial information records for Aguascalientes in the 1600s and early 1700, and I have noticed that for many people, especially for indios and mulatos, the couple's names are given as first names only, for example "Juan Diego" and "Maria Magdalena" with no family names for them or their parents. In other records, the data might be something like "Juan Diego hijo legitimo de Marcos Hernandes y Ana Maria"; in this situation can one assume than "Juan Diego" is actually "Juan Diego Hernandes?" However, I've also seen many cases where the information might be something like "Antonio de Silva hijo legitimo de Juan Marcos y Maria de Silva," which would suggest that this assumption may not be correct. A situation like "Juan de Silva hijo legitimo de Antonio de Silva y Maria Ynes," is also common.

There are numerous cases where the name is Juana de la Cruz or Maria de la Cruz. Is "de la Cruz" considered a family name or part of the first name? There also also other names such as de los Reyes, de la Trinidad, and so on.

I realize that Spanish and Mexican naming practices are complex, and the "rules" are often not followed, but can anyone shed some light on the practices in this time period.

George
Pleasanton, CA