The instructions were moved from that wiki page into the manual between the time I posted the link and the time you visited it...
If ipodpatcher is telling you that there is no ipod connected, then there are various possibilities, which depend on your operating system (Windows, Mac OS X, Linux...).
But the most important thing is to ensure your ipod is in disk mode - i.e. that it's displaying the "do not disconnect" screen. If not, then there is no way your computer can talk to it.
If you're still having problems, start a new thread in the Apple Installation forum, giving as much detail as you can about what you've done.
To answer your other questions - no, you don't need to uninstall the bootloader, ipodpatcher will just replace any existing bootloader, and no, ipodpatcher doesn't touch the part of the disk that your music is stored on, so it should be safe.