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1a You need to go in an physically split your zones to have 1 RTU per zone.

1b Use the Air Wall construction and apply the Air Wall Zone Mixing measure to approximate air exchange between the zones

2a In OpenStudio constructions are inherited first from the surface, then space, then space type, then story, then building. If you want the same construction to apply to all interior walls, specify that in the default building construction on the facility tab. More detail here.

3a You interior walls should have adjacent surface boundary conditions. If you ran the surface matching script through the BCL measure and they still aren't matching, changes are there is a small gap between the spaces. Try running the geometry diagnostic script on your model to see if any issues show up.

3b Use the same construction for adjacent surfaces, otherwise you will get an error when you try to run the simulation.