Your printer should produce clear, black print. A laser printer is good, an ink jet is fine, but if you have to use a dot matrix, you should use its very best letter-quality mode. Most manuscripts do not include a letter or cover sheet. The exception might be if you have previously published work, in which case it's fine to tell the editor of it. Don't use a binder or staples.
Paperclips are acceptable, but usually unnecessary.
Set your margins at 1.5 inches on all sides. The upper left corner of your first page should contain the information that every editor is going to need. List your legal name, address, phone number, perhaps an email address, and your social security number. Editors need the latter in order to pay you. If you intend to publish under a pseudonym, you still need to give your legal name in this area.