Yes. Unless you opt to carb and just run the MSD Hemi 6, pretty much any system (MegaSquirt, FAST, Holley, Mopar Performance, etc) will cover both sides.
I agree, if you are going to modify the engine a lot, then go that route, but the amount of money invested is twice as much. If you plan to stay stock or close to it (cam swap), then go factory stuff.