Simple! Add a missile and a point defense weapon from the dropdowns above. You'll see two forms show up along with a graph. In the forms you can change various missile parameters like acceleration, maximum speed, and health. You can also tweak the encounter and evasion conditions to simulate anything from head-on, maximum evasive maneuvering to side-on, no evasion conditions. In the point defense forms you can see how many hits the weapon needs to kill each missile. You can also toggle the simulation to use the burst fire rate, which for Aurora's acts as battleshort toggle and for the other weapons is most effective in simulating instant first-shots. See the Sarissa vs. an Atlatl for an example of what this does.
You can choose multiple statistics to graph from the menu above. For the statistics with normal and an "ideal conditions" version, the ideal statistic assumes perfect shot accuracy. All other statistics incorporate the hit probability calculation into their calculations.
The graph provides some facilities for zooming and panning. You can also export the graph as an image for sharing with others. You can hit the Reset button to remove all your missiles and point defense options and start again.