There are two primary population systems in Caves of Qud, the legacy EncounterTables.xml system, and the ZoneTemplates.xml+PopulationTables.xml system. EncounterTables is older and we prefer to use zone templates + population tables these days, but much of the game is still populated via EncounterTables.xml.

Like ObjectTables, EncounterTables.xml supports Load="Merge" in the object root tag. This will append entries to that particular table instead of overwriting.

PopulationTables currently do not support modding, but many zone template encounters draw objects from dynamically created population tables. Check out the following tags in ObjectBlueprints.xml to see them in use: DynamicObjectsTable, ExcludeFromDynamicEncounters. Some dynamic population tables are created based on the base type of the object, so new objects will begin appearing immediately in areas generated with dynamic population tables unless they are tagged with ExcludeFromDynamicEncounters.

The unaffiliated cave systems are the only areas currently heavily populated with the template+population system.

Additional Info

Here's a thread on Steam where I discuss using encounter and population tables: http://steamcommunity.com/app/333640/discussions/3/358415738194955181/