This will get moved to Hardware soon, but in the meantime here's a short answer. The string tree is there to keep your strings low as they pass over the nut. The string should dip under it, which is why the screw is as short as it is. Loosen the strings that pass under it, screw it down, then retune. If the hole for the screw is stripped out you can glue a toothpick into the hole to give the screw something to bite into. No need to remove the string tree to change strings, leave it on.
The low E rattle could be a number of things, including the string not being seated in the saddle. Try pressing the string towards the body on both sides of the saddle to help get it to break over properly.
Oh, and a string tree is not essential, the bass will not blow up. But you may get strings trying to hop or buzz in the nut as you play. Best to leave it on unless you know it's not needed.