Jefferson was not instructed to free Belle, he did it as revenge against Regina for screwing him twice.
He wanted to make sure Rumple knew that Regina held her prisoner all this time. Like the BF said to Regina “you better run and hide.” 😀
How could Jefferson know the “exit” lead down to a secret underground facility? And how could he know the code to open the door? And how could he know to bring Tea filled with something (poison?) that took out the watch nurse? And how could he know which door Belle was in?
incidentally, it was kinda funny to see Sydney Glass locked in one of those rooms.
I think he has had 28 years to watch Regina. In all that time he may have been able to figure it all out. 🙂