BeerSmith makes the calculation based on the mash tun size you have in the equipment profile. Assuming it can handle 100% of your sparge water, you can tell BeerSmith what to do. In the Batch Sparge area, you would click on "batch sparge using batches that fill" and input the percentage you're willing to fill. Then unclick "use equal batch sizes."
If it still gives you two batches, click the "drain mashtun" box.