For my New York solo game, my friend is making a character who is going to make his own weapons using the rules in CC. As one of his knowledge skills, he came up with Gun Design. This would govern the design of small firearms only we decided (slug weapons only basically). I'm not sure how this skill would apply though, as the rules for gun creation are fairly clear. Should I allow this skill to complement his gunsmithing or not?

I certainly would. The tests are pretty easy anyway, so it's not really a huge boon. It'll just shave some time off, which makes sense for someone who's a "professional" gunsmith (which, for me at least, is represented by having the knowledge skill as well as the active skill; kinda like how a doctor needs Biotech and Medicine).

What if he used it like a decker would use program design skill. Roll vs. 4 and add the successes to the actual Smithing test or is it add the succsses in dice to the test? It has been to long since I played a decker.

I'd say it should be used just like any other Complimentary Skill. Number of successes on the Complimentary skill test, divided by two, added to the successes from the Active skill test, provided the Active skill test resulted in at least on success.