Yes you might need to swap axes to align the transport direction, but that will be needed anyway because the C axis (the transport axis in QuantumATK) is perpendicular to the sheet in the original system.
After the supercell operation as indicated above, it's very simple to make armchair and zigzag by noting that the new A direction is along the zigzag direction, and B along armchair, as you can see if you make some repeats (picture below).