I'm not that familiar with the history of Spanish colonization of the Americas, but I am pretty knowledgeable about the Spanish colonization of the Philipines. I can talk about the latter and maybe somebody more expert on the former can give their own answer and we can compare notes.

By the time the spaniards arrived in the philippines, its natives are divided into several political entities or states, that historians now label as "barangays". These states each have their own languages, form of government, trade partners, and even religions. This made it relatively easier for the spaniards to apply a "divide and conquer" approach in their occupation.

An early example of this happened during their capture of Maynila in 1570, where Martin De Goiti brought warriors from the Visayas islands to Luzon and employed their help in routing the defenders of the fortified settlement. The following year, Miguel López de Legazpi brought 600 natives from the island of Panay to fully occupy Maynila, which they then officially called the City of Manila in 1572.

In paper, the Spanish conquest of the Philippines was supposed to be a slow conversion through religion, as ordered by King Philip II, a policy influenced by the recent conquest of the Americas. But, with the archipelago being halfway across the world, that proved to be difficult to apply, and much more to maintain.

The Spanish soldiers resorted to corruption and abuse, despite the watchful eye of the Catholic Church. And despite the abolition of slavery in the Spanish Empire, the Filipino natives, called "indios", were basically treated as slaves. This was due to the implementaton of the "encomienda" system, where colonists, (and sometimes the church) were granted ownership of the land, and people living in it were compelled to work for the "encomenderos". By "compelled", I meant they were forced to work under threat of violence or religious blackmail. Some were paid, but most of the time, not paid enough.

This system of governance remained consistent up until Mexican independence in 1821, where the Philippine islands were finally brought under the administration of the Spanish crown in Madrid. (Before that, the Philippines was under the Viceroyalty of New Spain aka Spanish Americas)

On the other hand, intermingling between colonists (called "peninsulares") and the natives was encouraged. This resulted to a new social class called the insulares, or to be more accurate, the Filipinos. (to clarify, during the Spanish times, the natives were called indio, while those with mixed-blood, they were actually the ones referred to as "Filipino"). Eventually, the Filipinos started holding government positions, as they were most times appointed as mayors of their respective towns.

Each town's activities and social events were centered around the churches, and the Catholic church were not exempted from abuse. The Spanish friars would often throw "piyestas" to appease the populace and snuff out any attempts of rebellion. Everybody pretty much fears the friars, that even Jose Rizal made them the primary antagonists of his novel Noli me Tangere. Though entirely fictional, the book elaborated on the conspiracy that the friars were keeping the masses ignorant to keep them under line.

A lot of historians would say the social and economic status of the Philippines remained stagnant during the Spanish rule. It was not until its final years the islands started seeing some changes, even enough for some Filipinos to propose that they be given representation in the Spanish cortes (parliament). It all came too late though, as the abuses and corruption of the Spain eventually led to the revoution of 1896 that culminated with the Philippine Independence of 1898. USA buying the Philippine islands from Spain for $20 million.