The shoebill-runtime is one of the main core parts of shoebill. Shoebill-runtime will implement all the interfaces provided by shoebill-api. Without a runtime, shoebill cannot run correctly. Shoebill provide a official runtime, but you can also create your own, if you don't like ours. Internally, the runtime will call the native SampFunctions everytime you call some function like player.setName();
You won't have to manually use a runtime for shoebill. It is already included in the resources.yml, but you may have to change the version number if something changed.