When you take the runway for departure, note the takeoff time. It is common to start a clock or write down the departure time just before taking the runway. Once you've exited the pattern and are comfortably established in your climb out and heading toward your first checkpoint, you may enter an estimated time of arrival for each of your checkpoints.
As you pass each checkpoint, note your actual time of arrival and record the actual time enroute. Knowing the actual time you passed each checkpoint and the distance between each checkpoint allows you to calculate your actual groundspeed. You can then adjust your time and fuel burn estimates, if necessary.
Below is what the navigation log might look like after the completion of the example flight...
