I have an item I created in the hop profiles named "Whirlpool Pause." I add this in and put in the whirlpool time to be the expected time for chilling down to the temperature where the first whirlpool addition will be made PLUS the full whirlpool steep time. This then starts as soon as the boil is over and the first whirlpool addition alarm goes off at the expected time and usually pretty close to the correct temperature.
Because it is listed in the hops profiles, I can remember to add it in as I am adding my hops to the recipe.