Order plugins are responsible for conversion of your source into one or more actual certificate orders. The default behaviour is that each renewal generated a single certificate. But in some cases, e.g. when you are close to the 100 domain limit, or you don’t want visitors of one site to be able to see other host names, you may want to split things up.
Of course this is also possible by setting up multiple renewals, but with proper use of source and order plugins the burden of managing certificates for different sites and domains can be greatly eased.