Basically its just two different companies, way back in the 50s one Miss America winner refused to promote the swimsuit brand, she wanted to be taken seriously as a singer. Then the brand in question founded the Miss Universe and Miss USA competitions.
Miss USA competes at Miss Universe and tends to be used by girls who want to work in entertainment, acting or modelling whereas Miss America remains solely a scholarship programme so tends to get more academic contestants. Also Miss America doesn't compete at any pageant internationally.
Miss America also has a talent segment to the competition which Miss USA does not.
Miss America is open to Puerto Rico and the Virgin Islands along with the 50 states + D.C.