UFO!!!
I see you used a separate sphere for the cockpit window.
Try this instead...
delete the sphere,
Select a few of the underneath faces,
Region Extrude them using their Normals' axis, about halfway from the sphere's height,hit Shift-D to repeat the action once,
Once extruded,don't deselect the top face(s),
Hit Numpad's + to grow the selection unto the bottom,
Hit S to smooth the extrusion and don't deselect yet,
Change the selection type to Vertice,
RMB menu choose Deform/Inflate and play a bit with it until you get a spheroid shape,Tighten as well if needed and tweak.
There you got a solid one mesh model.
Everyobdy wants to be loved,But no one loves everybody...