There aren't any limitations on point totals programmed in (yet). So you can exceed the maximum total points.
Under Active Skills, you can increase points and it'll calculate correctly. You need to select a group (it really doesn't matter which one) in order to activate the group values. In order to activate other sections like spells or complex forms, you'll need to select the appropriate skill.
Under Qualities you can select Adept, Magician, Mystic Adept, and Technomancer. Nothing stopping you. The Magic heading will be set to the last one selected.
Under Nuyen there are two lines since each point value is different along with the maximum number of points you can spend.
You don't have to enter any values in the blanks for the Knowledge or Language Skills. Just the points matter.
The number fields use the plus/minus to change values. You can enter in a value and the build points may not update until you click a button or leave the field. You can also put higher numbers in a few of the fields and it'll take it but it'll adjust if you hit the plus.
In other words, it's not perfect. It was created to help my players convert characters and not as a character generation script. It may get there though as it's somewhat silly not to finish :)