Because Autonomous Underwater Vehicles (AUVs) have limited perception and communication capabilities, designing efficient AUV flotillas is challenging. Existing solutions are often strongly related to (1) a specific kind of mission and (2) the nature of the considered AUVs. So, it is difficult to reuse these approaches when switching to another mission context. This paper proposes a generic multi-agent based layered architecture for designing and specifying AUV flotillas at a high level of abstraction, regardless of the AUVs characteristics and skills. To this end, an organizational model is used to ease and regulate interactions between heterogeneous AUVs and combined with a behavioral reactive approach for limiting communication.