What's the best practice for texturing assets? The manual says 'combine your assets into 1 mesh and 1 materiail/texture whenever you can'. The only examples of uv mapping/textures are in the FPS tutorial resource from the main site, this seems to be what they do. The trouble with using a texture atlas is you can't add or change textures like you can with 1 texture per set of uv's.
That is indeed the best practice and should be implemented where ever possible. I'm not really sure what else to add as your question is very broad. I'll offer any advice I can in an edit if you could be more specific.
Using a texture atlas is a pretty standard approach for any game development regardless of which IDE or Engine you use.
There is no reason you can't pro grammatically swap out images and textures at runtime with an atlas - just make multiple versions with slight alterations.
Also combining meshes and maps is "When ever you can" - if you can't then just make up for it by optimizing even harder in some other area or asset :)