Regardless of the time of day you decide to fly, the ticket price will remain around the same. Book flights from Flint to Sioux Falls as you normally would.
These are just IATA (International Air Transport Association) codes. They are used in aviation to identify and differentiate airports. That’s why a Flint Bishop Airport to Sioux Falls Joe Foss Field Airport flight would often be abbreviated as a FNT to FSD flight.