There are two special, built-in application types, ExperimentRun and ExperimentRunOutput. The first step in a protocol should be of type ExperimenRun, and the last step should be ExperimentRunOutput. The corresponding protocol applications should having matching types. Almost all other types will be set to ProtocolApplication, which you could consider to be the default.

If you have specialized needs, you can create a module that registers one or more org.labkey.api.exp.RunExpansionHandler instances. There's a little documentation on this at https://www.labkey.org/Wiki/home/Documentation/page.view?name=experimentIntegration. Based on the type, the server will check if there are any handlers to invoke. If the server doesn't find a specialized handler, it treats it as if it was a ProtocolApplication type instead.

There's nothing special about the SamplePrep type - it should probably be switched to the more standard ProtocolApplication instead.

Josh