Which Flowmaster catback do you have, American Thunder or Force II? I have the Force II and I don't think the MDS is that bad at all, at least compared to when I had the Blastin Bobs on mine. If you have the American Thunder then there's your problem, no resonators. You could always have some welded on but then it'll quiet the exhaust up somewhat, too. Some sort of drone is always going to be there with the MDS. I've even read from some with the Corsa exhaust that's supposed to get rid of drone all together that it's still there, although it's a lot better than other exhausts.
As far as brand of shorties, don't get the Flowmasters just because you have a Flowmaster exhaust. I don't know of anyone running those on either Charger forum I'm on, probably because they're super over priced. It seems JBA is the most liked brand for shorties and it'll pair up just fine with the Flowmaster exhaust. That's the route I'm going with mine sometime this or next year. JBA shorties, JBA hi-flow mids and my Force II exhaust. That's just my opinion though since I don't have them yet.