From Heraklion Airport, to travel to any town or resort in Crete (Chania, Rethymnon, Agios Nikolaos, Hersonissos, Malia, etc.), you do not need to go through Heraklion, certainly delaying the start of your holiday due to the heavy traffic you may meet.
The best way to leave Heraklion Airport is to use the National Road. On leaving Heraklion Airport, follow the wide road which runs from the airport exit to the National Road (red arrows on the map)
The first exit onto the National Road will take you into the lane heading to Rethymnon and Chania, while the second, a few metres further along, will take you into the Agios Nikolaos lane.