Q. If I have an embedded woa with all frameworks embedded, how should I deploy the webserver resources split install bundles stuff? Should they still be separate in usual layout and "not embedded" or should I construct an embedded bundle that mirrors the directory structure of the application bundle (only containing webserver resources of course)?

A. You can pass in a parameter to your app that specifies the path relative to your webserver document root to find your framework WSR's (-WOFrameworksBaseURL). By default this is /WebObjects/Frameworks. Instead you can set this to /WebObjects/YourApp.woa/Frameworks and then link or copy in your WSR's into that tree.

The woapplication ant task has a parameter named "frameworksBaseURL" to set the WOFrameworksBaseURL. See WOApplication

A. Another option is to build your projects with maven. Per default the build produces two tar.gz's. One with the app and all jars (frameworks) embedded and one with the webserverresources.