Yes, the DuoCharge is meant to maintain ONE other battery or battery bank. The EchoCharge is also meant for one other battery.
I don't see why you couldn't use two such devices, though. I'd probably put an EchoCharge on my start battery (like I've had on my boat for several years now), since the start battery requires very little charging to stay topped off; and put the second device -- larger like the DuoCharge if you like -- on the bow thruster batteries, because they're likely to eat a lot more AH than your starter will take.
Note that when the bow thrusters are in use, or any other load exceeding 30A, the DuoCharge will not supply current but will shut down for a short time, then will test to see if the heavy load has been removed. If so, it will begin normal charging operation.