There are two places where OSGi's settings can be changed:
Module specific settings are managed through the OSGi module facet settings.
In the facet settings you first have to decide whether you will edit the manifest files yourself or whether you want OSGi to create it with bnd from the dependencies on other modules and libraries.
When you decide to maintain the manifest file manually, OSGi creates dependencies on modules and the framework instance bundles in the module where the manifest file is changed. Here you take charge of the OSGi dependencies between your bundles and OSGi tries to match them with corresponding module dependencies.
Letting OSGi generate the manifest files for you is exactly the other way around. You develop your application as you would develop any other application in IntelliJ IDEA. You add dependencies on other modules and libraries and OSGi tries to translate those dependencies into OSGi dependencies when running your bundles.
If you are maintaining the manifest file yourself, you have to tell OSGi where it is. You can change this location for each module, or you can define a project default in the project settings.
Each time a module is compiled, OSGi creates a bundle JAR for that module. This JAR is used when running an OSGi run configuration. You can change how the JAR is named and where it is put, but for most cases the created default should be OK.
The created JAR contains the compilation output and the manifest file - either the manually maintained or the one created by OSGi. Sometimes you will need to add some other files that need to be copied into the generated JAR. For Eclipse RCP bundles - or plugins as they are called there - you will need to add the plugin.xml. You can do this in the table listing additional JAR content. The first column takes the path to the source file relative to the content root of the module and the second column takes the path to the destination file. So since the plugin.xml of an Eclipse RCP plugin normally resides in the root of a plugin, you will type in plugin.xml for both columns of that entry. Future versions will provide a file chooser to choose the source file.