You could do SIMPLE EVENT COUNTING (for NI-TIO hardware), in which the active edges of the source signal will increment the value of the count register. You can choose whether you want the active edge to be rising or falling by software. When doing simple event counting, the gate and the out signals of each counter are not used.
For taking a look at more specific literature, I would recommend to take a look at this link: Event Time Measurements
Over here you will find tutorials and example programs that can give you an idea on how to implement your final project.