Start by clicking on the nose cone icon. A window will pop up to set the nose cone parameters. Select shape, length, diameter, material type, whether it's filled or not. Click on the shoulder tab and set those parameters.
Once you have the nose cone set close that window and click on the body tube icon. A window will pop up with the body tube parameters. Select length. diameter, wall thickness and material type. If it is a minimum diameter rocket click on the motors tab, check the "this component is a motor mount" box, click the select motors tab, choose the motor to be used in simulatons.
Next do fins, centering rings, inner tubes, engine block, chutes, streamers, shock cords etc. Each icon will bring up a window with a new set of parameters to be selected.
Once you have "assembled" your design select the flight simulations tab. Click the new simulation tab, select simulation parameters and click the run simulation tab. Sim data will be posted, you can plot the sim by clicking on the plot simulation tab, there are more parameters that can be selected.
The best way to become familiar with the program is to sit down and start working with it. After an hour you will be familiar, after a few hours you will be a pro. It is a very simple and intutitive program and a useful tool for designing rockets and running simulations.
There is much more to the program but if I were to go into every detail this post would become a users manual. If you post specific questions I will be happy to answer them to the best of my abillity.