Yes exactly Karl. You can pause sim and Cigar Box will also pause. Un-pause the sim and Cigar Box will resume recording the flight. (No intervention is required in Cigar Box).
Additionally, if you are on the ground, and wanted to pause for a while after landing at a stop-over or midpoint, you could either pause the sim or more realistically, being on the ground, you could just shut down the engines after parking: and as soon as you kill the engines of your aircraft Cigar Box will pause/stop ticking. Later as soon as you restart the aircraft engines to resume your flight Cigar Box will resume the flight clock for that flight.
One difference when on the ground: When you pause the sim, the time of day is also paused but for more realism when you kill the engines (but don't pause the sim), the sim "time of day" keeps ticking.
Later when you start up the engines the time of day are reflected in both the sim and Cigar Box pirep/flight logs. Either way works but for a bit more "time of day" realism when on the ground shutting down the engines work great.
Norm