After every few rounds and before a competition you should deep clean your muzzleloader. First you take the muzzleloader apart by taking out the pin and pulling the muzzle off of the stock. 
Then get a bucket of hot soapy water. 
Take the nipple out of the muzzle with a nipple wrench. Then put the muzzle in the water and use your rod to push the hot soapy water up and down the barrel with a clean patch. 
After it is clean, completely dry the muzzle then use bore butter on a clean patch to wipe down all of the metal inside and out. This keeps it from rusting. 
Then put the muzzleloader back together and you are ready to go.