I just got my first muzzle loader deer too. I was sitting on a log in a cedar swamp watching a trail 25 yards away. I had my CVA Plainshunter loaded with 90 grains of FFg Elephant and a .490 round ball. A big doe came in about 1/2 hour after I sat down. She put her head down facing head on to me. I was sort of elevated on that log. I shot dead center in the neck so the ball angled down through the chest. One shot, she tipped over.
She was down, and certainly wasn't getitng up, but she did pick up her head a few times and was still alive for the moment. I had my .69 flintlock pistol with too. I had it loaded with 40 grains of ffg and 6 OO buckshot. She was down, and her legs sure weren't working, but she kept picking up her head and gasping. Rather than leave her to suffer, I decided to try the pistol for a finishing shot. I touched it off from 10 feet away. Only one buckshot hit her between the ear and eye and then she expired.
I'm sure the finishing shot wasn't necisairy, but I felt better knowing she wasn't suffering. I brought it with so once I fired my rifle I would have just such a finishing shot without reloading. It was surprising how few of those pellets actually connected with her. I don't even know if the pistol sped up the process or not.