There are many different ways to clean a muzzleloader depending on the make and model of the rifle. You might want to refer to your manual for the proper steps to clean it.

I personally use a good quality solvent, bore brushes, and lots of patches. I work that barrel and all parts over until they are spotless. Then I re-oil it all up, re-grease the breech plug, and re-assemble the rifle. After wiping it down again with oil it is set to go....