Well I'm not sure about all the ins and outs of it. The auto patcher wasn't working for me but I think you can push the 3 files or include them in the Rom. Anyways I'm kinda n00bish but all the info you need should be here http://forum.xda-developers.com/showthread.php?t=1357056
hope this helps. Oh by the way I'm on #2 1.6 and everything is sweet. BT pairing is working like a champ. I was able to get pdroid patched using the mod for broken out Rom but it has the smooth scroll and data throttle remover included. If you want to check that patch out I can upload it to drop box and give you a link. Thanks for your hard work.