Having a box right at the end of the pipe is mostly looks, but might affect the sound a little. Currently I have a V8 muffler under the bed (tray) and a stainless cannon at the end. Sound is OK.

Ultimately for optimum performance I would put a resonator (small muffler) under the cab and a large muffler somewhere after that, wherever there is room. Generally the larger the muffler the quieter the exhaust. For maximum power at say 5000-6000 RPM you'd want a pipe to end about 33" from the valves. Easy way to end the pipe is use a resonator, because then whatever you put behind that point does not affect HP. You can fit huge or loud or quiet muffler at any spot after the resonator.