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Could you please put the pen over the book?
Could you please put the pen on the book?
Could you please put the pen upon the book?
Could you please put the pen above the book?
Could you please put the pen up the book?
Which of these sentences is/are correct?
For the incorrect ones, I hope you add extra information like, “This word (‘over’, ‘on’, etc.) cannot be used that way, but it could be used this way:” and give an example.
2) Could you please put the pen on the book?
is the most likey way someone would say this. 3) "upon" is also OK but is more likely to occur in literature. These refer to placement.
1) Could you please put the pen over the book?
4) Could you please put the pen above the book?
These refer to location. This would imply the pen is located above the book, which would not be likely in the setting of your examples, but could be possible with other wording. For example:
Could you please put the pen on the shelf above the book?
Finally -
5) Could you please put the pen up the book?
does not make sense in this phrase. "up" refers to inside in a sense.
An example where it would be OK:
Could you please put the medicine up your nose?
There is a significant difference in meaning if you are talking about the pen and the book as objects that you are just locating in space... vs. getting a pen ready and poised to write in the book.
Let us say the pen is just an object that might serve the purpose equally well whether it is capped or uncapped, and its nature as a writing tool is irrelevant. Then simply upon/on would likely mean the pen is resting on the book and touching, due to gravity. above would probably suggest not touching but being in a somehow "upward" direction. (Like hanging from a string in three dimensions, or perhaps placed on a table "above" the book as it is seen from a photo in its defined orientation.).
The construction up the book is bizarre; it suggests some kind of slot into which the pen could be put. You might argue that if a closed book were pierced through the pages along the binding that someone "stuck the pen up the book" but that is awkward. up the (whatever) has "vulgar" associations as a phrasing for almost any (whatever)--at least today.
If it is an instruction about a pen in readiness to be writing in a book, then perhaps the more important thing to point out is the nuance of "book" itself. The word in isolation is typically used to mean something pre-printed that you aren't to mark up...and there are special categories invoked for the kinds of books you are "supposed" to write in (workbook or coloring book).
In that sense the best answer may be "Keep the pens off the books, or you'll hurt their resale value." :-)
If you wanted to tell someone to get their pens ready to write in a book, you'd be clearest saying:
"Open your workbooks to page 3, and touch the tip of your pen to the center of the page."
Because if that is what you are trying to say vs just positioning objects (as for a photo shoot, like @J.R. suggests) then none of the choices you mention convey that meaning well.
The best fit might be onto, which indicates movement:
Could you please put the pen onto the book?
