I use a stopwatch to help avoid running the boiler dry. Measure the amount of water you put in the cold boiler. Heat up, and run motor for 5 minutes. Stop, drain and measure amount of water left. Water start-water left/5=ml of water used/minute. Figure out how much water you want to leave in boiler, then divide the rest of the water volumn by your ml/min to get your minutes of run time. Be aware that bench-derived minutes will be different from on-the-pond minutes. Running w/o pond water resistance on the prop or paddle will use up boiler water faster, so bench derived minutes-to-run are probably conservative.
Plan to leave 1/4" of water in the bottom of a simple, tubeless boiler. Plan to leave at least 1/8" over horizontal tubes in a horizontal boiler, don't worry about vertical tubes or horizontal tubes if they are in a vertical boiler. It'd be better to leave 1/4" over horizontal tubes, but a model boiler may be so small that you won't get much steaming time. You will just have to be more careful when running a horizontal boiler since you are leaving yourself less latitude for mistakes in timing.
By shutting off the fire before all the water has evaporated, you will protect your soldered joints from melting. A silver-soldered boiler is more resistant to dry-boiler damage than a lead-soldered boiler....but it's never good for any boiler to run dry, so don't push your luck. Be conservative (run for short times only) until you get a feel for actual boiler water usage. This will depend on what you are doing on the pond, the air temperature, how well you lubricated the machinery, and other factors. So, every pond run will be a little different to a lot different...all part of the steam operator experience you will gain if you pay attention to what's happening each cruise.
With gas fuel (propane or butane or a mix), you can make an rc gas cutoff. That way, if you find that the boat is in the middle of the pond when it's time to stop steaming to protect the boiler, you have a way to shut off the fire. You may need a rescue boat to retrieve your steamer in this case. The gas cutoff is a "braces and belt" recommendation; if you pay attention to your watch, you won't need it. See the Steam Tramp thread for details.
I agree with all Mogogear said. Controlling the fire allows you to run longer because you are not losing water due to the safety valve blowing. As he said, this is a problem for start/stop activities peculiar to tugboat ops. It's also a problem if you set the gas valve too high at the start of your cruise. The way I handle that one is to keep the first cruise of the day close to me so I can bring her in and turn down the fire (or turn it up) if I guessed wrong about steam production rates needed for the day.