You may loose a very little low end with the 3 in. system, but overall (city/highway) you will see improvement. The biggest problem with the Hemi breathing adequately is the stock exhaust manifolds. Although they port match the heads (1 3/8 in.), internally the ports dump into each other from front to back and exit into a 1 7/8 in. ID collector. With the firing order as it is, not all of the cylinders scavenge through the manifolds adequately, especially the driver's side. Once into the single system they should scavenge better than a dual system. I would guess that you have a pretty big drone issue on yours without any other silencing other than the Magnaflow. Which one do you have. On mine I have two 12 in. glasspacks (one in front of the Magnaflow and one in the resonator position) and a 14589 Magnaflow, and it is just barely passes the wife test, especially when the MDS is active. In V-8 mode it's not too bad.
06 GCO, Dk Khaki, QDII, Flshing Hi 3rd Bk Lt, MDS "ON" Lt, Airtab Vortex Gens, Debadged, Fumoto Drain Valve, BT Catch Can, Chopped EGR Tube, SRT8 CAI, K&N Filter, Sonnax Trans Line Press Booster, SC Tuner W/Adv Trans Tune App, DS Tuner, Cust tubular hdrs w/3 in Magnaflow/Xlerator AP Exh Sys, Bilsteins, SRT Springs/Sways, Cust Eng Cvr, SRT8 frt/rear bumpers, FRI Sidewinder Cam/6.1 valvetrain, SLP 25% UD Pulley, BBK true 90mm T-Body, SOS Ign Coils w/.060 spark plug gaps, SRT Reps with 265/45&295/40X20's.