I shoot only traditional M'loaders, and I never remove the breech plug unless it is absolutely necessary (hasn't happened yet). My philosophy is that every time you loosen a threaded item, it turns a little further when retightened to the same tension. Pretty soon, things don't line up properly, especially on octagonal barrels, but you must line them up for the gun to function, so you end up with a looser breech plug.
The best way to clean the barrel with the plug in is to remove it from the stock, remove the nipple, set the breech end in a container of hot, soapy water (black powder is water-soluble). Then run a patch up and down with a cleaning jag on a rod. The tight fit of the patch to the bore will create a suction, pumping the soapy water back and forth through the breech plug. You can loosen fouling a bit with a wire brush first, but the hot, soapy water will do the trick by itself. Dry everything thoroughly afterward, and wipe with rubbing alcohol to displace the remaining moisture. Finally, oil the bore (I use CLP Break-free), and you're done.
It is sometimes necessary to wipe fouling with a moistened patch during repeated shooting. A properly fitting cleaning jag is an essential piece of equipment for a barrel with only one open end.