I am not sure that I fully understand what is happening but will take a stab
at helping anyway (which is always dangerous).

There are 2 places in the DD wizard you can assign portions of a building to
different air-side HVAC systems: the 1st screen of the air-side HVAC
definition (I ignore this), and screen 14 of each Shell - the zone grouping
screen. What you can do in the 1st screen of the HVAC is limited and is
superceded by screen 14 - the zone grouping of the shells.

So, my practise is to:

1) Define separate zone groups for different HVAC systems in the shells
definition (if all zones in a shell are the same HVAC system, that's fine)

2) Define all the air-side HVAC system types

3) Go back to the zone grouping screen (DD wizard shell screen 14) for
each shell and assign the HVAC system for each of the zone groups in that
shell.

I hope this helps - let me know if I missed the mark.

Cheers,

BF