Whenever you submit an application to an organization, it is standard to submit a resume AND a cover letter, and any other documents they request (writing sample, transcript, etc.).
A cover letter is a letter application. You are letting the organization know that you are interested in the position AND what background and experience you can bring to the position. The cover letter helps you to tie together your skills, achievements, and experiences.
A cover letter is written to a specific organization, not a generic document. You can create a prototype cover letter, which you can then easily personalize to a specific organization. When possible, it is ideal to send the application to a specific person.
In the cover letter you should illustrate how you have used the skills for which the organization is looking. Instead of just stating you have the necessary skills ("I possess strong writing and organizing skills. I also have excellent research and computer background."), go a step further. Show how you successfully used these skills/achievements in past experiences. The best indicator that you can do the job is to show how you have already used the skills they are seeking. Cite achievements and examples. Remember that you do not need to have used the skills in the exact, same setting of the job that you are applying to. You can transfer the skill from one setting to another. Showing concretely how you successfully achieved the skill will illustrate your background effectively to the reader.