Richard,
You do not need need to recreate your ontology.
In order to use SPIN with your model, you should import into it the SPIN namespace – simply drag and drop the file into the Import tab of your ontology. The file to import is under TopBraid/SPIN directory – spl.spin.ttl. This will make it possible for you to add SPIN rules into your model.
You can also create a new SPIN/RDF file (take a look at all the import options in the wizard to figure out what you need to add) and then drag and drop your ontology into it as an import. This way the new file will contain only the SPIN rules and your underlying file will remain unchanged.
It is up to you which approach to take.
Once you have SPIN rules, you can run them. Inferred triples are placed in the runtime inference graph. You will see all of them in the Inference tab. You can then assert them into the file you have opened or you can use Export>TopBraid Composer>Export/Merge/Convert RDF Graphs and save the inferred triples as a separate graph.
Running such inferencing can be automated as a web service, but this would require a TopBraid Live server or, at minimum, TopBraid Composer Maestro Edition. And, yes, the server would need to be running to execute the process.
Regards,