de2 fpga gpio question

The simplest idea would be using the inputs directly to control 2 specific application functions.

For example you can implement a counter and use one input for start/stop and the other for reset. If you have a 7segment display or LEDs you can direct here the counter output; this is the classic starter design for beginners.

If you want something more difficult you can connect the two pins to rx and tx of a UART interface and then transfer data to and from the board.

Your fantasy (and device resources) is the only limit.