Very easy. When that happens one set is always primary and the other vestigal or secondary. They use the bathroom of the primary set of genitals.
If those genitals are male and they feel like a female, what then? Tough luck I guess?
If their skin is white but they feel they are black, tough luck for affirmatice action I guess?
If you are born with fully functional legs, but have Body Integrity Disorder should all your medical records reflect that you are a paraplegic and have a state provided wheelchair?