Question: When sending a resume to a company’s website, should a cover letter be part of the resume document or should I write the letter as the email and just attach the resume alone?
Answer: Great question. That depends on what you want the cover letter to do.
If you want it to highlight things not in, or obscured in your resume, it goes as the first page of the resume. It MUST be in the same document as the resume. (I suggest you also redo your resume to highlight important points.)
If you think it has to be read to get someone to even open your resume, it goes as the email that your resume is attached to. NEVER put it as a second attachment to your resume. If you do, it will be ignored.