Whilst on the topic, how could I make this model more game-ready overall? I'm doing this to just practice.
As for spheres - remove bottom halves that are inside geometry and then just attach using ctr+j to join it with the main mesh. As for game ready - one idea would be to actually bake the spheres as a normal texture and use it to imitate bumpiness.
For gameready object i would not use subsurface modifier at all, instead I would make a denser model with subsurf (like one you have already), and then I would retopo it - using shrinkwrap modifier I would create a low-detail version.