Resonators and mufflers are largely the same thing, but theyre called different names because theyre doing a slightly different job.
Generally speaking, the resonator you have and the muffler you speak of are both straight through mufflers. The difference comes in at the frequencies they target. The length, cross sectional area, and packing material all go into how the resonator/muffler perform and the frequencies they'll take care of. A round muffler will target a very specific set of frequencies whereas an oval muffler will target a different set. This is because the radius from the center of the pipe(s) going through the muffler case to the wall of the muffler on the oval muffler vary based on the height/width of the muffler and this radius is part of a function that when taking into consideration the speed of sound and the radius at a given point on the case of the muffler.
To answer you question most directly, what a resonator is doing is reducing rasp since it's performance target is much higher frequencies (small distance from center of pipe to resonator wall). A muffler, as goalieman mentioned, targets lower frequencies and thus most often will quiet the general volume of the exhaust.
At this point, you need to ask yourself what exactly is your end objective is - more specifically, what do you want the exhaust to do? If you want the loudness without the rasp, keep the resonator and no muffler. If you want to have the rasp with reduced volume, get rid of the resonator for a traditional muffler (wider and shorter will work best all around). If you want to take it all down a notch, add a muffler.
Now, I will make mention that you'll likely end up with more audible drone by adding the muffler to the system since you're going to be reducing/emphasizing droning frequencies and there are relatively easy ways to counteract them. However, that's a lot more SCIENCE and money spent to achieve that.
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