I see this sentence:
Dividing a large writing project into separate files has disadvantages, though, especially if you are doing your own desktop publishing from within Word.
I am confusing that why two prepositions can be used together?
Good question. I have edited it to say "prepositions". "Propositions" means something else (a common mistake).
Some prepositions, especially from, can precede a prepositional phrase that begins with another preposition. It is easier to understand for an example like:
This means that the cat was under the sofa, and the speaker took the cat from there (the space below the sofa).
Doing your own desktop publishing from within Word is a more abstract and nuanced example. It is similar to saying you are working from home, and more specifically, you are working from inside your garage. In this case from does not indicate literal motion, but it emphasizes that you are virtually "going to" work from the inside of your garage.