The user manual gives an overview of all program features, explains the input parameters and simulation results and also contains some additional background information.
The Theory Manual is still a work in progress and is intended for developers and interested users. It covers the theoretical and technical details behind the software like the mathematical bow model and the numerical solution methods.
Simulations can be used to evaluate bow designs, but they don't actually tell you how to design a good bow. These are some good resources about bow design:
The Traditional Bowyer's Bible, Volume 1, Chapter 3: Bow Design and Performance by Tim Baker. All common design choices and how they affect bow performance are explained in a very practical and understandable but nonetheless precise way.
The article on bow design from the crossbow building wiki is also a good read. It is geared towards crossbows but most of it also applies to bows in general.
SuperTiller by Alan Case is an Excel spreadsheet for simulating the statics of user-defined bows. It's probably one of the most well-known bow design tools.
Woodbear's Selfbow Design Sheet [zip] by David Dewey is an Excel spreadsheet that calculates the necessary dimensions for a bow according to a user-defined stress distribution.
BowCAD by Joachim Gröger and Chris Goetz was a commercial attempt at bow design software. At one point they were even offering different kinds of licenses on their website http://www.bowcad.com/. Unfortunately it seems to be no longer available.
DrawCurve Calculator by Chris Snyder is a utility program for visualizing a bow's draw curve and calculating the stored energy.
x-Ballistics is a browser based application that can simulate the exterior ballistics/trajectory of arrows.