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Good question... I have always been taught and have always put my heading on the right hand side if not centered on the paper.
Maybeeeeeeeeeeeeeee , because its easier to look at instead of looking to the right. :] I would prefer it to go to the upper left , to me it looks better.
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What you are referring to is actually called a running head (running because it appears on every page). It is primarily used in academic and journal article writing for the purpose of identifying pages of a document in the event that they get mixed up with other papers. Some say that it serves to provide the title of the document to the reader in case they didn't read the title page. This happen in the peer review process where articles are given to the board of peers doing the reviewing sans title page. This ensures a fair reviewing process, after all, if one of the reviewers happens to know the author his or her review could be biased.
The running head is on the top left of the page for a couple of reasons. First of all, in academic and manuscript writing, we only write on one side of a page. Even novelists submit their work to their publisher single-sided. Therefore, the heading and the page number are always going to be in the same place on each page. It is the typesetter's job to adjust the heading and page number when it comes time for publication and the work will be printed on both sides of a page. Knowing this and knowing that it is Western custom to bind books on the left, where is the most sensible place for the page number? On the right, that way if we need to find a page quickly it's right there on the right where we can thumb through the pages quickly. If the head were there and the page number were to the left we would actually have to completely open each page to find the page we wanted. The head contains no information that would be strictly needed in identifying anything in the document and it never changes, so putting it on the right provides the reader/reviewer no benefit.
The other reason is that most academic papers and manuscripts are submitted without being stapled. The reasons for not stapling are many. Other than the problem that you describe about the staple covering the head, the biggest and main reason for not stapling is because if the article goes published the staple must be removed for the typesetter to do his or her work. Removing the staple from a day's worth of article is time consuming and mars the paper making it difficult to leaf through. If you've ever taken the staple out and had the papers still stick slightly together at the puncture marks, then you know what I'm talking about. Another reason for not stapling is that in academic journal articles, the page count can be quite high. I have read articles in journals that were as high as 45 or 50 pages. Try putting a staple through that. Although I did have a few teachers in college that wanted us to staple our papers, most did not want them stapled. They usually wanted us to turn them in in a clear plastic folder with spine to the left.
So really the problem you describe only happens at the lower academic levels (high school, under graduate). Academic format rules (APA, MLA, CMS, etc.) are designed with publication in mind and therefore are geared toward graduate and post-graduate work. Lower academic levels adopt these rules to prepare students for writing at those higher level.
Hope this clears this issue up for you. ;)