the bio matter needed for a 125 gallon long tank has to be massive specially for any tipe of african cichlids. reason cichlids produce very large amounts of waste. and yes biological filtration should be under water. expose to the air the biomatter will die of very quick. plus your HOB are essencial because they produce lots of air exchange and if they have bioweels even better. ihave a 125 long with (2rena filstar xp3)(2emperor400)(1emperor power head)(40 gallon sump 600gph running mostly biological filtration) this aquarium has a total of 40 cichlids mix. I do a 30% water change ones a week.