I do it completly different for different situations.
For example for hand made default levels I normally split them into parts where either is a asset change in the levels or where a new design part of the level begins. When you work with several people you also could divide by designer.
Then you can create specific lighting setups for the complete level which you can switch on runtime, for example for level on day or night. This is done by a specific type and there can only be one active at once. Don’t remember its name currently…
If you want to create procedural maps the approach is different. I this case you can not use prebuild lighting iver all your levels, when using static lights. In this case you have to prebuild sublevels (complicated) and use movable/stationary lights in many cases.