I've written a bit about this before, and will be quoting from two earlier relevant answers and connect them in the end. Your question's spectrum is very broad, as there were important differences between e.g. the British and French empires -- my answer will focus stronger on Spanish colonialism, and try to highlight a few differences.

Here I wrote on organisation and justification for empire:

In the Spanish overseas possessions, colonies were built with their own viceregal administrations that answered to the Crown but retained a high degree of autonomy vis-a-vis the metropolis – in part due to the distances involved and related difficulties of communication at this point in time. Mixing between Spaniards and indigenous people was part of colonial life from the conquests onwards. In contrast, the British looked rather to building settler colonies with a focus on extracting resources for use in the metropolis. Relations with the native population were tabooed and (as far as I know) rather uncommon. Another difference was related to the economy, as the highly monopolized Spanish economic system, with all trade from the colonies running through Cádiz/Sevilla, was not adopted by the British.

Anthony Pagden (in Lords of All the World) has examined the discussions on Spanish, British and French empire, and highlighted how contemporary theorists of empire followed developments in the respective other states closely: Putting it briefly, a main justification for Spanish colonization was connected to the empire's extraordinary size (under Charles V, and under different circumstances under Philip II); this was in turn connected to the emperor's mission of bringing 'civilization' by way of the Catholic faith to his tributaries. Pagden then traces the beginnings of the Leyenda Negra through British and French writers, who underlined the extreme violence committed by the Spaniards (supposedly extreme in comparison to their colonial rivals). Lastly, he shows how these intellectual discussions influenced the later (British & French) empires' differing justifications of conquest and empire, focusing rather on their right to “unoccupied lands” overseas, rather than the Spanish religious justifications. In these different ideologies behind colonization we can find, I think, an explanation for the different organization of the earlier and later empires, taken together with economic considerations. I summed up some of Pagden's main points here, but the whole work seems very interesting for your question.

Here I look at the Spanish casta system -- I'll quote the most relevant part:

This importance of religious justification [discussed above] would be one distinguishing factor from later, more scientifically justified forms of exclusion as practised by the modern colonial empires (although religion remained as one argument). Another main difference is that the Spanish casta system was relatively fluid in comparison: Although the highest rungs of colonial society were (mostly) reserved to people born in Spain, creoles gained increasing access to important offices. What is more, ethnic and casta categories were often consciously used, e.g. by mestizos or creoles, in order to attain higher positions (as argued by Salvador Velazco in “Visiones de Anahúac”). This shows that legal focus on blood purity could often be modified in “real life” - a marked contrast from race discourses that from the 18th c. onwards started focusing more on skin colour and other physical attributes than on blood/lineage.

Summing up: I'd like to highlight a few differences between the earlier and later empires. Regarding organisation, the Spanish colonies had more autonomy and mixing between Spaniards and native people was very common from the start; British settler colonies focused more on the export of resources and for the most part British and native people remained apart in colonial hierarchies. This is connected to the Spanish casta system (based on degrees of descendence from Spaniards) being less rigid than the systems developing from the 18th c. onwards, that focused on skin color, anatomy etc. Regarding economy, the Spanish trade monopoly through Cádiz/Sevilla fostered resistance by colonial elites, and stood in contrast to later empires' freer trade models (e.g. allowing for trade between colonies). Lastly, on justifications of empire the Spanish highlighted the unprecedented size of their empire in connection with a mission to "civilize" the native people through religion; the French and British had followed the difficulties connected to these Spanish discussions and thus in contrast emphasized their right to supposedly “unoccupied lands” overseas.

The quoted answers contain more suggested literature, but Padgen's Lords of All the World might be a good starting point for comparing different discourses on empire-building.