As far as the columns marked Volume U.S. gallons is that how much I want to end up with or the amount that I pitch into after boil.
That's the volume in the fermenter when you pitch the yeast. I have to ask, though - are you leaving so much behind in the fermenter that it would make a difference?
As far as the growth factor and viability columns I'm a little bit confused as for what values to input.
"Growth factor" lets you decide whether you want to make a large starter with fewer (usually one) yeast products, or a smaller starter beginning with more yeast. Just move it around until the number of packs/vials and the starter volume match up with what you're able/willing to do.
The viability calculator is my only real gripe with the MrMalty calc, since it assumes a linear reduction in viability over time. For the most part, though, if your pack/vial is reasonably fresh you can just put in the production date and let it estimate viability for you.