Right-click on 'library'
Go to file...add to library...add folder.
Select the folder that you store your limewire downloads in.
Then, go to file...add to library...and look at 'by monitoring folders'.
I think that certain folders are included in your library by default (I don't remember having to add any).
These include folders like 'my music,' 'my videos,' etc.
If you don't want to transfer your limewire downloads to these folders, add your download folder to the list of monitored folders.
Hope this helps!