One cover letter for two positions with same employer, or one cover letter per position?

I'm currently an undergraduate student applying for internships this fall. Some of the postings on the online student jobs board are for the same employer, through the same contact, and require the same application materials.

For example, two of the jobs are for the same employer, have the same contact, and both require a cover letter, a resume, and two writing samples. To apply, I must submit these materials via email.

Should I merge my two applications in this scenario into one, by sending a resume, the two writing samples, and a single cover letter that handles both positions? Or should I send two separate emails, each with their own copy of my resume, writing samples, and cover letter? The cover letters for the two positions are identical except for the position name, if that makes any difference.