The best place to get started familiarising yourself with the architecture of the Toolkit is to clone one of the demonstrations- either the Database Visualizer or the Flowchart Builder might be a good option, since they are fully-featured apps. If you're using Vue, Angular or React there are versions of these apps that use the appropriate library integration that ships with the Toolkit.
Alternatively, you might like to start with the documentation. The Data Model and Basic Concepts pages are the best places to start looking around. In a nutshell, the Toolkit uses a directed graph as its core data structure. Every app that has a need for jsPlumb - which is to say a need for the ability to connect entities - can be thought of in terms of a directed (or undirected) graph.