The Cover Letter
Every proposal needs a cover letter, though it should be brief — no longer than half a page in most instances. If you're sending your proposal at the request of an agent or editor, remind the recipient of that at the beginning of your letter. Then give a brief description of your proposal, reiterating the important points, particularly about potential readership and sales. Close with a thank-you and a call to action. As in your query letter, you should express simply an expectation of further communication, nothing more.
If there is anything new — changes in current events that make your topic even more timely, for instance — note this information in your cover letter. It shows an agent or editor that you're on top of the things that affect your proposal, and it can be an additional selling point.
Many authors include their original query letters with their proposals. This isn't a bad idea; some agents and editors find it handy in reminding them of why they were interested in seeing the proposal to begin with. However, if you choose to do this, you also need to include a cover letter, and the wording of your cover letter should be different than the wording of your query.
As with your query letter, make sure you have the agent's or editor's name and title correct in your cover letter. Use a standard business salutation; you're still in the wanting-to-impress stage, and you don't want to turn off the agent or editor by getting too familiar too quickly. Reserve the first-name-only greeting for when you've got the contract.