Weird - the new 3 Ducks web site says that it's at the Commerce station. Anyway...
From Charles de Gaulle, take the RER train "B" (blue line) into Paris.
To get to the 3 Ducks, get off at the St. Michel-Notre Dame station.
Option 1: Take the underground conveyors to the Cluny/Sorbonne Metro stop (it's all connected to the St. Michel station) and get on Metro line 10 (gold) toward Boulogne/Pont de St. Cloud. Get off at the La Motte Picquet Grenelle stop and transfer to Metro line 8 (violet) toward Balard - go a stop or two to the Commerce or Felix Faure stop and get out there.
Option 2: At the St. Michel station, get on the RER train "C" (yellow line) westbound. Get off at the Invalides station. Transfer to Metro line 8 (violet) toward Balard, and once again, get out at the Commerce or Felix Faure stop.
To get to Gare Montparnasse from the airport, take the RER B (blue) all the way to the Denfert Rochereau station. Transfer to Metro line 4 (magenta) toward Porte de Clignancourt. Get off 3 stops later at Montparnasse.
Here's a decent image of the Paris Metro system, but you'll be able to get a much clearer map when you get there.