The AFCAD doesn't have any problems, and as explained so many times on the forum, we flagged all the non-cargo parkings as GA, in order to get rid of default ground vehicles, which conflicts with the scenery and GSX as well.
The Cargo parking are also all correctly flagged as RAMP CARGO so, if the Cargo airplanes you use have been correctly flagged as using the cargo ramps themselves (in their aircraft.cfg), they are supposed to go in the Cargo parking spots.
And, all the parking spots also have airline codes so, if the AI airplanes you use have been correctly flagged with their airline codes, they should go into the correct spots *by preference*
However, this assumes the parking radius is big enough for the airplane to fit there so, it's possible that if you have set the traffic density very high, the larger cargo airplanes are overflowing into the other terminals, because there all the largest parking spots have been already taken.