There are 4 potential files in question. The .iptheme or .iconpackage files have the information for what icon goes where from their corresponding .ICL file (or loose icons). The .ip file is a zip of those content files for packaging, to keep things smaller and bound up in 1 file for downloads.

When you create an icon package under Package Builder mode (the View menu) and save it, you're saving the .iconpackage and .icl. From the File menu, you can use the Zip option to package a selected icon package up as a .ip for uploading/distribution.