...are you able to have some objects share the base uv's, and then have some not share the second set of uv's? It's easy for the base textures to share space but on a lightmap, it all needs to be unique, so would i just make the islands tiny and fit everything, or can I have the first uv map shared and use individual secondary maps for each object?
What is the best practice for lights uv's on multiple objects? Maybe this is covered later.
I personally have never baked a 'lightmap' before. Maybe that's due to less experience with games for me, more experience with offline rendering.
But I think the answer is yes. For objects to share UV's they need to be identical meshes. So let's say you duplicated a crate a bunch of times in a game level. Each crate could share the same UV's for the crate texture but each would need a unique secondary UV map for its custom lighting info to be baked to. You should be able to simply add a new UV map per duplicated crate and bake individual maps to that second UV map.