This is an issue with all patch boxes . I use a combination of methods including some homemade wooden dies, assorted nylon, brass, and dead blow hammers. Small dents are somewhat inevitable and can be filed, out afterwards.
As for the hinge, Gary Brumfield has suggested it is best to do the bulk of the bending before cutting the knuckles, but I assume that is no longer an option. If you're using a factory made box you're already stuck with rather unsightly gaps inherent with the stampings that they use.
I try to bend the surface of the box while minimizing the amount of the bend to the hinge itself. It also helps to shorten the hinge pin allowing the ends of the hinge to be flattened and then filed to more streamlined look.
Jeff