It largely depends on whether you intend to publish the map for web only (in which case hyperlinks to separate maps will work) or in printed form (no hyperlinks).

I think you're right in thinking that putting the second floor on a different layer will make your life easier. Alternatively if you wanted entirely seperate maps, just save the original under a different name and redo the inside of the building of that one as the second floor.

Welcome to the guild, btw!

Ravs