Is there a file structure we should stick to with the modl file? For example, where should 3rd party jar files live inside the modl file?
They should all be in the root of the zip. Each will need a callout in the module.xml to indicate what scope or scopes to load into. This is generally handled by declaring a dependency in the pom file.
Some luddites still use ant to build modules, so cannot be more specific. 