The internal design of the pots is indeed to provide a water reservoir and also help watering.
You have the option of using 5" pots, which then sit on the "mushroom". You fill the top row of pots until the reservoir is full and the water overflows down drainage channels to the next row of pots.
The other option is to fill them with soil. Since I have the irrigation setup we felt this would be the better route as it provides more soil for the plants.