I kind of do ventilation calculation separately in Excel to get a good strategy to balance total exhaust and supply. Our state has huge exhaust requirements (much higher than ASHRAE) and this forces me to do more ventilation (transfer air) anyway. Trace has limits to how many rooms can transfer air into one bathroom for example.
If there are only a few exhaust areas, I use ventilation based on code/ASHRAE whichever is higher. Our code doesn't use the IMC area/people based ventilation, only people based.
Once I have my code-required flowrates for each zone I enter those as manual values in Trace for each zone.
you also need to document for code officials how you came up with your ventilation/exhaust. Each code also allows different transfers from locker to bathroom, shower room etc. Trace isn't really set up to deal with all that. these are items each code official may have a different opinion on as well.
You also have to fully understand all the data Trace (or HAP) give you. Especially if you have mixed heating (radiant and VAV reheat) etc. you want to manually adjust what you actually want to do.
Trace is great calculating the VAV zone requirements, OA, etc. but you should do it manually in Excel as well to be sure all is correct and you understand it. you can set one thing wrong in Trace, and it can be all wrong.