You don't say what OS you are using. I use XP, so it's really simple. Not sure about Vista.
Plug in the Flash Drive and your computer should recognize it as being an external HDD. What ever drive make note. Now go to your shared folder outside of Limewire. Now you will be able to either copy or move files to the Flash Drive. Just click on a file and select one of the 2 options. Now a drop down menu will appear and select the Flash Drive destination. Hope this helps.
If you select copy the files will stay on your PC so you can have them on both computers.