Funny glitch in that program is, if you have a toon at level one and try to assign the starting numbers to it, it say you haven't earned enough experience yet... so it disallows a level one toon to have 100/10/100/100/10/10 starting stats for example.
To add starting attributes you have to add them in the character design page/tab.
To add attributes from augs you have to add the augs then add them in the character design page.
So say to calculate what it would cost to get sword to 400 with 100str/coord you'd enter 100 str/coord on the character design tab under the primary attributes slot. Then you'd check spec sword. Then you'd go back to page one.