Cloth patched roundball is by far the most common load in smoothbores but for whatever reason I've just never gotten the accuracy with a patch that I got with the ball in a shotcup. I've owned smoothbores of .50, .54,. 56, .62 and .66 calibers as well as several 12 gauges. I've tried patched balls in all of them and none grouped so tight as the .648 ball in a shotcup and that load shot well in every 12 gauge gun I've ever tried, including factory choked double barrels. I generally loaded 3-3 1/2 drams of powder, two over powder cards and 1-1 1/4 ounces of shot and a thin overshot card. If I had occasion to change loads in the field I could just run the small end of the ramrod down to tip the overshot card, pour out the shot and seat the shotcup and ball atop the normal powder and wads. That can prove handy if one should encounter a deer while small game hunting. Yes you certainly can substitute a cloth patch for the plastic shotcup, I just never got such good results from a cloth patch, so far, but I'll keep trying.
I might add that I never use plastic shotcups with birdshot, just hard card wads, and when I have shot test patterns with them I have never found any advantage, certainly not the 20% improvement as claimed by many gun magazine writers.