With the license files, there are instructions on where to place the license.
INSTALL
krpano Flash Panorama Viewer:
Copy the "krpano.license" file into the folder of the krpano SWF file.
If the SWF file was renamed, the license file must be renamed accordingly.
krpano Tools:
Copy the "krpanotools.license" file into the folder of the of the
"krpano tools" programs.
OR
(in my opinion, the better choice)
you can use kprotect to place your license into the .swf and not have your license exposed on the internet.
The main difference between the two licenses are: the "limited" is in fact limited to the domains you specified when you ordered it. The "unlimited" doesn't have any restrictions and will work on whatever domain you place it on.
I hope I answered your question.