If the calculator doesn't ask how many cylinders, just use the actual engine size and other data, but multiply the result by 1.333.
According to Bell, the port area of a siamese intake should be 2-3% higher than the area of the intake valve as a minimum.
For a 1.94" valve (common for Gen-3 L6) that's about 3.04 square inches, equal to a rectangle 2.03" × 1.5" or a round port 1.97" ID.