Just like any other entity in EPT, use the EPT.<EptName> namespace for your JS modules.
web/public/jsmodules.JSModule.js, it will be available as require.js module
Similar to modules, there is also a
GlobalRegistry.js file available for adding scripts to
instance.js for load on every page. As with modules, this should be reserved primarily for detail registration.
You can submit the JS file to the running server as part of EPT.
JS modules defined in EPT won't be available for users outside the EPT's enterprise.