sounds like you have one like mine from Beeline apiaries. When I started my colony last July, I only had one hole open on an end. Lowes sells the right size black stopper to plug the holes. The colony has grown big enough this year that I have 2 of them opened. The middle one is not used quite as much as the original end one, but still plenty of traffic.
They have drawn out roughly half the bars. I think by the end of this summer, they will have drawn out all of the bars, and then the third one will be opened up for their use. Having multiple entrances doesn't seem to confuse them in the slightest. The brood nest is one comb away from the original hole on the end. Honey is being stored in the combs in the middle. As I open up the brood nest, the bars all get shifted down, so the honey bars will get slid toward the end.