Most of my downloads automatically go to the library, but some do not. how do I get them into the library

All downloaded or downloading files will go to the library. Incomplete files found in incomplete folder. Downloaded files found in Saved Files folder. As for Shared folder, check your settings. Only files shared will go into there & be visible AFAIK. LW's menu bar, Tools>Options>Sharing & at bottom of window is Download Sharing. Check this option if you want all downloads shared & shown in the Shared folder. If you don't have this option ticked, then it may take a while before they show up in the Shared folder.

Another small complication is if you right click a download & choose a different download location. However, with the above option ticked it should still show in the library.

I am still confused. I have the songs downloaded it limewire but I don't have the Tools option on my menu bar

Are you using windows or mac. If mac, you will find preferences option under LimeWire name on menu bar.
Keyboard shortcut for Mac OSX is ⌘ , (Command/apple key & comma) which is the same for most OSX programs.

Most of the songs automaticvally go to the library, a bunch have not. I just downloaded another song and it went to the library. All songs sitting waiting to upload say"complete 100%.

Yes that's the way LW works. If a file is only 50% completed downloading then it will remain in the incomplete folder until it is able to 100% download & then LW will move it from the incomplete folder to the Shared folder.