I assume you are talking about the caliber of bullets and sabots. If so....
The 44 cal. will load 10 times easier but will fail with high pressure loads such as 3 Pyrodex Pellets. The 45 cal will take the pressure but be prepared to work at getting them down the barrel.
I shoot 44 cal with 2 pellets and get great groups. I have tried the 45 cal and will never use them again, bullets just should not be that hard to seat. Matter of fact, I got a great deal on my Encore because the previous owner bought 45 cal bullets. The first one loaded so hard he was scared to shoot it. Pulled the breach plug and unloaded it. Aw what a deal I got, I could not tell him there was nothing wrong with the gun.