Once you enter the simulation phase, the geometry primitives from meshing are not translated to this section. You are given the option to make new primitives but these relate to new functions more for boundary condition regions and stuff like that. So it is ok to leave that section blank, same goes with topological entities, it does not need to be filled up but it is useful to group up surfaces to assign boundary conditions to them. Only the things that have a red circle are needed (you need to define a material and boundary conditions).
It seems to me like maybe you would benefit from some tutorials that can help you answer all these questions. Here’s my suggestion:
Also check out the air conditioning sessions that are pretty much the same application as the church problem you are doing and they offer videos too.
Good luck!