Open up one of the decoction based profiles, and see what a decoction based mash step looks like. I don't remember, and I dont have beersmith near me. the step type will be something other than infusion---decoction maybe? Set your target temperature, and BS2 should tell you how much mash to remove and boil.
remember that when doing a decoction you want to remove the grain, not the liquid. The liquid is where all the enzymes are, so if you boil that you will kill off some of your enzymes. I have a large pot strainer that I scoop my grain into with a ladle. Then I drain the liquid back into the MLT. Once you've collected the desired amount of grain: put it on the stove and heat it...stirring constantly (don't leave it, or it will scorch!!!). When it starts to boil, reduce the heat slightly and keep stirring. It takes about 5 minutes or so to get the whole grain bed up to boiling temperature. then add it back to the MLT, and stir it into the main mash.
I usually collect a little extra grain for my decoction because the scooping, straining, and stirring will loose some heat. 10% extra above the BS2 calculate value is a little security against undershooting your target temp. if you end up a little high, you can always stir for an extra minute to drop it back down.