you guys may be "atheist" but i think you're still deists at heart. if you want to raise your child an atheist, it's as simple as avoiding all religious practices (that don't come that often anyway.) do something else on a sunday morning, before starting on a meal, at 3:00PM, at 6:00PM, and before going to sleep. even practicing catholic will be excused for missing out on those things.

as to actual nurturing, textbooks, and other media will show you the ABCs of it, from health and hygene, to character and values building. i studied in public schools and we were kinda heavy on character ed (i'm not claiming to be an outstanding result though.)