BEopt doesn't explicitly allow modeling multiple air conditioners, but you can approximate it by using the average efficiency (weighted by the floor area served by each AC). Unless you override it, BEopt will automatically autosize the AC to meet the entire cooling load, even if that means the capacity is larger than whatever the largest residential AC on the market is. You'll likewise want to enter average duct leakage/insulation inputs.

Note: There is no need for multiple thermal zones just because there are multiple air conditioners, since all finished/conditioned space will be maintained to the same setpoint.