In the first two boxes at the top you'll need to input two numbers. Those numbers are the size of the beam and the divergence of the beam from the diode minus any optics. The diameter of the beam is very small so a number such as 0.01 or 0.001 can be input into the first box. This only matters if you are making an optical system for a raw diode. For a laser with an optical system measure the width of the beam and estimate the divergence of the beam. the reason being is the expander will be placed well within the Rayleigh Length. within that length the beam only expands 1.4 time it's original diameter or 1.4 times.
In the second box you'll input the divergence. A protractor is useful to do that if this is done for a raw diode. Now we get to the next set of boxes. Let's keep it simple; and use only two lenses, one a negative lens, the other a positive lens. In the first box input the focal length of the negative lens ex. like this -6. This app assumes all lenses are positive unless designated otherwise. Spacing of the first lens is arbitrary if this app is used to make a beam expander. If this is used to make an optical system for a raw diode than spacing of the negative lens will have to be place close enough that the beam directly from the diode is not truncated. Now, input the second lens which for example has a focal length of 50mm, decrease the spacing by a small amount ex. to say 44.9, watch the graphic, increase the spacing by a few millimeters, watch the graphic and the numbers below the graphic. Start at a spacing of 50mm. You'll also notice several columns listing information, the one that is important to understand is the one which reads "Beam Diameter at Surface" what that means is the diameter of the beam as it meets the positive lens. You'll need a lens of a larger diameter so the beam is not truncated.
If you want to collimate for lowest divergence watch the graphic. When the lines representing the beam run parallel that's the lowest divergence. More questions just ask.