If you select the "Tivo Official" protocol in KM it will use the built in protocol, but your device upgrade will be twice as big as it would if you were to use the hacked protocol.
However, you could let KM figure out the hex codes for you, then you could program 2-byte keymoves using hex codes.
It's generally a good idea to ask JP1 questions in the JP1 forum as there are more JP1 experts congregated there.
Rob
http://www.hifi-remote.com