You can tie two systems (duct to duct) together but the whole mess is VERY fragile -i.e. as soon as you connect/change systems again all associated and attached get all redefined. The easier solution is to create a mixing box family but you still only have a few built-in systems to choose from (SA, RA, EA). ...Yes the systems can get a bit tricky -i.e. exhaust air, tempered air, supply air, and return air but you're just going to have to "not fully connect" (if you establish all those duct systems)--but then you loose part of your calculations--or deal with the built-ins (SA, RA, EA)--potentially loose colors on the screen-.
FWIW: My systems are SA, RA, EA, & OA. and these are only for colors on the screen (in working views). The built-ins are really only to establish "symbols" (Cross, Slash, Wye) in the rises and drops and for calculation purposes.
Generally speaking in an average duct system you can have:
Exhaust (Lab/Chemical/Biological & General)
You <-- Grain of salt.