The way I've set LimeWire up is by writing an alternative runlime.sh script. The script creates a .limewire directory in the users home, changes to it, and runs limewire. LimeWire then writes it's configuration and the Incomplete directory into ~/.limewire.

You can see the script (for LimeWire 1.7) here:

http://www.cyberspace.org/~kohl/limewirelinuxhowto.html

I've just installed 1.8 and you need to modify the script to make it work. I'll write a 1.8 update in a day or five. ;)