Yes, you were able to check/uncheck checkboxes for different archives inside one project. When checked (used="true"), than the archive will be build, while unchecked (used="false") the archive will not be build. Actually, making comments in the packages file to exclude parts out of packaging is a solution, but an ungly one: ) E.g. parts that are commented out does not appear in the Project archives view.
To help you to remember, this is an entry in .packaging:
<archive destination="lib-runtime" exploded="false" name="juicystuff.jar" used="true">
<folder ... />
</archive>