Starting with In-Portal 5.0.0 there is ability to create "theme.xml" file under "_install" folder in theme. This file holds meta-information that is used to interact with theme templates. You can even create "_install" folder under each module sub folder in one theme, e.g.
/themes/theme_folder/_install/theme.xml- in-portal file
/themes/theme_folder/in-commerce/_install/theme.xml- in-commerce module file
Right now I'm integrating (infusing pure HTML slice-up with In-Portal tags) new In-Commerce theme and I don't have any "in-commerce" module sub-folder to place it's theme.xml into it. So I've decided, that you can specify alternative module directly in theme.xml file to place all module-specific theme information into single theme.xml file.
Here the sample:
In the above example is the contents of /themes/theme_folder/_install/theme.xml file and you can see how "section_design" and "item_design" have "module" attribute specified.