Basically that. How do you planify on grouping UVs from a set of objects - atlases as for my understanding - on large scenes to also ensure decent texel density to bake? You do it by area? - idk, kitchen, room 1, room 2 - by type of object? by size? Hope that makes sense @_@
You do it based on what is likely to visible at the same time. Generally speaking related assets will be batches together - eg. the components of an air conditioning system will be atlased together and you won't include the underside of a truck