It depends on the design of the exhaust.
Ideally true dual exhaust you come straight out of one exhaust manifold or performance header on one side of the engine, you map it back through to a muffler to the rear of the car then you mirror the pipe configuration to the other side. this would give you balanced exhaust output and tone from each cylinder bank from each side of the engine. with each side of the engine having its own muffler and exhaust piping (some people will tie the two pipes together in the center of the vehicle creating an "H" pipe design popular in mustangs)
The setup I imagine your looking at runs both sides of the engine through one muffler then exits the muffler through two ports. so if one pipe exiting the muffler is longer than the other one then yes you would have an imbalanced sound from left side of vehicle to right side of vehicle; however, with the improved aggressive tone your not going to notice and you should be happy.
I would suggest a flow master 40 or 50 series muffler these two options will give you the throttle sound your looking for without the issues you were concerned with. Which ever muffler you choose the vehicle won't become obnoxiously loud due to the 4 catalytic converters plumb'd in your exhaust between the muffler and the engine. hope this helps