The only way I know of including sub packages, is first to create your package (or open one already made by another author).
I accomplish this by doing the following > Open IconPackager > click File > New Package > click Open (or click new to create your package if you havent' done so already. Note: you should repeat theses steps if doing the latter making sure to exclude clicking new) > now once you have a package open, the "Sub Package option" will become selectable. Select the "Sub Package option" > Click Add New > find the package/packages you want to include > click OK. Now all you have to do is choose Save-As and name the package.
You will be able to choose your sub-packages using a drop-down menu when selected in the IconPackager menu.