The actual Aquarium is at the top of the map. From the ticket counters at bottom left you have to walk across a long courtyard to reach the actual entrance, passing food stalls (including a Starbucks) and two different pools which from the map you might imagine are for animals but are just for kids.
There are two wings in the building (Waters of Taiwan on the left, and Coral Kingdom on the right), and then a third separate building (Waters of the World) which only has an arrow pointing in that direction on the map.