In my opinion, the following is the most efficient way, and has always worked for me:
1 - Create a folder with all your icons needed for the package, and then open and expand it so that it occupies 1/2 of your screen vertically. Note - I suggest viewing them in "List" view (found under the folders "View" menu) and having them named in a way that is clearly identifiable to you.
2 - Open IconPackager and then use the "View menu > Package Builder" command to open package builder. Expand the package builder so that it occupies 1/2 of your desktop screen verically.
You want the two windows (1 is package builder, and 1 is the folder containing the icons in list view) to be side-by-side vertically.
3 - Now just drag-n-drop the icons from your folder onto the text location (such as 'My Documents'), or icon image in package builder. As long as the result of each drag-n-drop is an icon with a little green '+' sign next to it, you are in business.
4 - Once you have changed all the icons you want changed in package builder, use the "Save" button in the package builder toolbar to save your package.
5 - Close IconPackager, and then reopen it to refresh the list. Your new package should now be listed.
6 - Select the package and apply it to test. You can also use the "Preview" button to verify all looks good in the preview.
Important - I have noticed that IconPackager can be tempermental if you try to load a package and then open package builder to 'edit' the package. In some cases, this results in a corrupt package where some icons get misplaced. I do not know the cause, but I suggest building a new package for any editing, and removing any previous version of the package out of the "C:\Program Files\Stardock\Object Desktop\IconPackager\Themes" folder to a temporary folder in say "My Documents" to hold until you successfully create the edited package.
This last procedure is time consuming, but in the end should result in an uncorrupted package that you can upload without fear of issues for other users.
I hope this helps. If not, post any issues and I would be happy to test here.