Like pdr said, "Don't do that."
The cover letter plays a very specific role in the application packet, which is to create a clear path between the job ad, you, and your resume. The cover letter is used to show the links between what's in the ad and what's on your resume, not only to show how you match (prove to them you're a perfect fit), but to show the employer that you pay attention.
The cover letter is your chance to make the employer want to read your resume, and therefore if it comes behind the resume, you're either a) not doing that or b) placing a burden on an already overworked pair of eyes who has to go hunting for your cover letter (not a good first impression).
If the ad says send a CV and cover letter, you send both; if you put them in one PDF for some reason, then put the cover letter first (it is a COVER, after all...).
If the ad does not say to send a cover letter, then you decide whether you want to use one or not, but if you do, still put the cover letter first.
I would also note that your assumption that electronic documents are printed is not a particularly good assumption; as a hiring manager I can't remember the last time I printed something.