Depends. If it doesn't look like it matters, I just go into whatever one is closest. But if there are two, and the game seems to be hinting at a certain one, I'll go in the other one first. I always go where the game isn't telling me to go first, or if the other way looks like progress.
That said, if it's a game where the character can use these bathrooms, you get an effect from it and/or you need to use it once in a while, and it doesn't matter if I go into either of them, I'll probably go into the one opposite of my character's gender. Just for amusement.