first copy the krpano licenses into the tools folder
then start the kprotect tool
now it depends - to you want to build an domain limited swf and/or do you want to build a swf with embedded xml - select the "swf protection mode"
when select embedded xml or "embed startup xml" check the "embedding" tab and see if all files that should be embedded are there, maybe add or remove files
then check the options in the "protect" tab, e.g. you want to enable/disable parameter in the html file or the javascript interface
then press the "generate protected file" button and save the new swf file (the licenses will be automatically embedded)