The easiest way to make use of physical buttons is to use the digital I/O on the NI 6229 cards.
In Simulink you would need to get the digital input block for the NI-6229 card. If you were to want to use the first 2 channels then you would specify in the block to use 1,2 as the input channels.
The buttons created would need to be connected to PO 1, 2 on the BNC 2090A board. The connection can be bare wire into PO 1,2, or you can use a piece of wire to connect PO 1 to User 1, and PO 2 to USer 2, then use BNC connectors to User 1 and User 2. The buttons can be 5v and it’s up to you if they should got high or low on a press. You would specify in your stateflow/simulink if you were looking for 0 or 1 as the hit.
I hope that helps. Let me know if you need more details.