I'm not familiar with the multimodule-content-package-archetype but a good structure for this is to have a main pom that just points to the other modules, put your bundle modules in a "bundles" folder, and the CQ content package module, if you need one, under "content".
So with bundles foo
and bar
you'd end up with
pom.xml
bundles/foo/pom.xml
bundles/bar/pom.xml
content/pom.xml
where content/pom.xml
has dependencies on the foo
and bar
modules and embeds their bundles in the content package, in install
folders that CQ picks up when the content package is installed.
I suppose you can rearrange what the multimodule archetype generates like this, and then add as many bundles as needed under "bundles".