First, make sure you have all the correct class levels (or equivalent, at least) and fill in all the bonus spell caster levels in the "Prestige Classes" tab. This tab will only appear if you have a prestige class. If you do not have a prestige class, don't worry about it.
Second, make sure you have your relevant ability score correct in the "Race & Stats" tab.
Last, go to the "Spell Sheet" tab, and select your spell casting class in the combo box in the upper left corner. After doing this, you should get an hourglass for somewhere around a minute. If you go back and change anything, hit the "Re-Run" button located under the spells/day and save DC table.
I found this tool really confusing as well, but it's extremely useful once you get the hang of it.