I don't think it's possible to have two different folders for limewire to save files to but to activate the folder you need to go into tools, options, savings and than click browse and select the folder you want limewire to save files to.
If you want to delete it make shure you did not select it as your shared folder make shure you are not sharing it to change this go to tools, options, sharing. To remove it from there click on it and than click remove at the left. When you try to delete it make shure limewire is not running and it should work.
if you want to create a playlist just share the folder go to tools, options, sharing, and click add locate the folder and click ok and than click ok on the options menu. You'll have top save files to the folder yourself though