When sending your cover letter and resume electronically, try to find out if the employer would prefer them as attachments or in the body of your email. If you can't determine a preference, send them both ways in a single message.
Although not usually required, you may want to follow up the email with hard copies of your cover letter and resume, (unless specifically asked not to). When submitting copies by mail, it's preferable not to fold them. It's also a good idea to bring copies of your cover letter and resume to any interview.
Dear Mr. Rogers:
I am applying for the position of Grant Writer at Friends of the Earth, which I saw posted recently on Idealist.org. I'm extremely enthusiastic about this opportunity and believe I am well qualified. My cover letter and resume appear below, and are also attached; please let me know if you have any trouble opening the attachments. Thank you for your consideration.