When you book the flight (either on airberlin.com or through an agent), you may specify seat reservations.
However, there is one weirdness and one nuisance:
- Nuisance: once a seat reservation is made, you cannot change it online. You will have to call the airberlin hotline to make changes. After I managed to tell my travel agent to book not 32F but 2C or the like, everything got better :-)
- Weirdness: if you do not make seat reservations and check in with luggage for a first segment of a booking, you cannot get a seat online for the return flight anymore. The option will be displayed, you can select a seat, and then you'll get a notice that looks like the programmer threw it in five minutes before the beast went live.
Regarding your hotline experience: if there are disturbances (like in April/May with massive delays and cancellations through TXL) or if there is high demand (summer time, special holidays), you will have to wait a long time to get through. Try to take care of this through your travel agent, not airberlin.
Cheers,
--j.