The scheduled ventilation setpoint temperature controls the scheduled ventilation will reduce flow rate when the setpoint is reached.
The ACH is the maximum flow rate that is then modulated by the schedule.
Hence, the scheduled ventilation module is useful if you have measurements or simulation results from CFD that you would like to bring into Energy Plus.
The natural ventilation module creates a flow rate based on buoyancy and wind driven models. Using both the scheduled and natural ventilation together to then match a total ACH is difficult. If you know what the flow rate is - or should be - I would use just the scheduled ventilation module.
Maintaining the relative humidity levels is then done with the schedule. You can generate and hourly array schedule with Archsim using weather data and some larger or smaller conditionals to compose a control schedule.
I hope this helps.