iTunes will show a playlist called ??? LimeWire tunes or something similar which simply reflects what files you have in the LW download folder. To remove this, go to LW's menu bar, Tools>Options>iTunes>Sharing & disable the iTunes sharing option. Then relaunch both LW & iTunes & you won't see that playlist any more.
For problem 2, it sounds like you have iPod set for automatic update of playlist. What auto-update does is remove all songs from iPod then update with the new playlist. I would instead highly recommend Manual updating of your iPod. See the following link & watch the video & also click the Learn more link:
http://www.apple.com/support/ipod/tu...tarted_t3.html