Well once you unlock them, you start with one Honeycomb and you
have leave a Male Combee there. Eventually, it will produce Honey
that you can use on the Honey Tree. After some time you will be
able to build two more Honeycombs and have a maximum of five Male
Combee residing there.
Also, if you leave a Shiny (Male) Combee they have a chance of
producing Super Honey (which is Red compared to Yellow)