Widgets can be added either between begin() and end() or using add.
Fl_Window *win = new Fl_Window(width, height, "title");
win->begin();
b1 = new Fl_Button(0, 0, 120, 30);
win->end();
b2 = new Fl_Button(130, 0, 120, 30);
win->add(b2)
The FLTK docs are generated by doxygen so basically they are only as good as the comments in the code (which is not bad for doxygened documentation). You'll get the same problem with code documented with javadocs and the C# autogenerated XML documentation.
Have you had a look at http://seriss.com/people/erco/fltk/ and http://seriss.com/people/erco/fltk-videos/ . They are the official "helper" web pages. I learnt a lot just by looking at the cheat sheet and examples in the distribution tarball test directory.