are you going FFIM? or stock mani? if you are using the stock mani then just follow the stock routing for the hotpipe and go through the snorkle hole for the coldpipe. check this out:
http://www.supramania.com/forums/showthread.php?t=12711&highlight=hardpipes
also there is a writeup in the referance section, like the last page, that shows how to make your own hardpipes.
cant help you if you are going ffim. i think you would have to move the battery but i have no idea cuz i'm gonna be using the stock mani for a while.