Hi KierAnon, I think that you can do as you prefer (more precisely it depends on the kind of scene that you are setting-up) but I think that the drawback with merging two big surfaces (as walls and floors are) is that you have to set a really high LightMap resolution for the merged mesh, as in general, walls and floors (as separated mesches) needs quite-high lightmap resolution for giving good shadows results.
What kind of scene are you setting-up?