If the PTAC uses a heat pump for heating, use BEopt's Mini-Split Heat Pump category. Otherwise, use BEopt's Room Air Conditioner category (in combination with Electric Baseboard if the PTAC uses strip heat).
If you ask BEopt to autosize HVAC, it will calculate different sizes for each apartment. But if you hardsize the equipment, only a single size can be specified for all apartments. One option is to do two runs, 1 with 3/4 ton and 1 with 1 ton, and then combine outputs for the two runs by looking at unit-specific outputs. There is a dropdown on the output screen where you can see outputs on a unit-by-unit basis instead of the entire building.