Phil, all you have to do is set the MIME/content type for the resource to
application/zip and IC will recognize it as an archive-type static resource and offer the option to convert it into a resource bundle. Generally you'll want those in a separate source root (this is configurable in IC under
Validation & Deployment settings). IC will create and register the source root for you when you convert your first resource into a bundle.
You can absolutely add those files to version control and I would recommend doing so as the master version of the static resource's contents.
By default any time you save a file under a resource bundle IC will automatically recreate the corresponding static resource file and deploy it for you. Again, this is configurable in the same location, but IMO enabling it results in the most intuitive workflow. Similarly IC recognizes wen a retrieved static resource file is managed locally as a bundle and extracts it for you, either for comparison (Retrieve for Merge) or for update (Retrieve/Refresh). The goal is that it should be a very seamless experience of working with resource bundles.
Obviously if you go this route and you have some type of non-IDE automation for deploying your metadata, you'll need to augment those processes for resource bundles. For example, if you use the Force.com Migration Tool (ant tasks), you'd just need to have a pre-sf:deploy step that archives your resource bundles into the corresponding static resource files. That way you'll have the same experience in your scripts as you do in the IDE.
Hopefully this answers your questions, but let me know if you it doesn't and/or it leads to additional ones.
Regards,
Scott