This collection of model simulations/apps provides covers various aspects of infectious disease epidemiology from a dynamical systems model perspective. The software is meant to provide you with a "learning by doing" approach. You will likely learn best and fastest by using this software as part of a course on the topic, taught by an instructor who can provide any needed background information and help if you get stuck. Alternatively, you should be able to self-learn and obtain the needed background information by going through the materials listed in the "Further Information" section of the apps.
The main way of using the simulations is through this graphical interface. You can also access the simulations directly. This requires a bit of R coding but gives you many more options of things you can try. See the package vignette or the "Further Information" section of the apps for more on that.
You should start with the apps in the "The Basics" section and read all its instruction tabs since they contain information relevant for all apps. Most apps are arranged in a way that the best approach is to go through each section, and within a section from left to right. Some apps are out of order. If an app builds specifically on earlier ones, it is usually stated in the "Overview" section.