Here are a few things that I've worked out with ST.
I can answer a few question you have.
1. To start you can click on the prestress button which starts at 0 which should be the BACK of the bow not the belly.
2. You can modify the result with Design Operations but I prefer to hand enter numbers in the Modified profile to shape the limb the way I want. To me it is simpler. Though the "Offset X & Y" is handy to move the limb up for a 3-piece bow.
3. You can rotate the limb using the rotate function (be sure you have the start at 0 and the end at the last number of sections your using) to try different limb pad angles.
4. Then you set your draw length to what you want and the brace height plus 1.75" because it's measuring from the back of the bow.
This should get you started. What really helped me was to take a bow I owned and copied it on a grid and got the measurements from it. Then I hand entered those in the Modified Profile and experimented with that.
5. The poundage that comes out on the Report page is only 1/2 the actual weight. It doesn't say that anywhere in the manual but I was told by Alan that is the weight that show.
6. Say your weight that comes up in the report is too heavy you can decrease the thickness proportionately using lets say .9 in the Design Operations and clicking on the thickness choice which will reduce the thickness 10%
Clear as mud right?
Play with it and watch the outcomes. :D