well, you have to have the location of jre in your $PATH shell variable.

that should take care of some of your problems.

Otherwise, I've found that running limewire from a directory other than the directory where runlime.sh is located causes problems (running it from a menu item, or a symlink in /usr/bin, etc).
I haven't had a chance to figure out how to fix that, but it seems from the docs that there's something you can do to runlime.sh and your jre configuration to alleviate this problem.