For the Performance Rating Method to achieve credits under EA credit 1: Optimize Energy Performance, your minimum ventilation rates must be the same for both your proposed model and your baseline model unless you meet the exception for demand control ventilation. This means that you will decide to model your proposed model ventilation as the building had been designed then you should model it exactly the same in the baseline in most cases (unless you meet the exception listed in the standard).
Run the Proposed alternative to obtain the total, building, outdoor air intake flow, and then divide that number by the square footage of the building to obtain a cfm/sq ft value. This value would then be applied as the ventilation rate for all rooms in the Baseline alternative. Note that the Standard 62.1 inputs in Create Templates and Create Rooms must be set to “No” and the system ventilation flag under the Create Systems / Advanced button, will be set to "Sum Room OA Reqs" in Baseline alternative so that the program does not run through the standard's calculations again.