Okay, maybe CP2000 has more insight on this, but here's my understanding of the two.

The Miss America Organization began in Atlantic City as a means to promote tourism after Labor Day eighty some years ago.

The Miss Universe Organization was created by Catalina Swimwear about fifty years ago. The Miss Universe Organization also oversees the Miss USA and Miss Teen USA pageant competitions and venues usually change from year to year.

State winners in the Miss America local pageants are called "Miss [State]".

State winners in the Miss Universe local pageants are called "Miss [State] USA". Teen winners are "Miss [State] Teen USA".

...So yes, there are two separate state pageants held.

The Miss America Pageant also conducts a talent portion for their contestants, while the Miss Universe Organization does not.

Also, the Miss Universe Organization is owned by the none other than Donald Trump.

Hope this helps.