How do I make V-not-V questions with prepositions?
I assume the V in 'V-not-V' means 'verb'. However, in the second group of the sentences you gave, you are repeating the prepositions (从把往离), not the verbs. Of course, it's also possible to ask questions about prepositions, but if you are trying to practice the 'V-not-V' structure, the 'V-not-V' structure should be used, shouldn't it?

That be said, for some of the sentences, the 'V-not-V' structure are not the best way to form questions. And some of the first group's sentences themselves are not natural to my ears. Here is the most natural way (in my opinion, not necessarily the only right way) to say them and ask questions about them:


  他从北京回来。
  
  他是不是从北京回来？
  
  我把水喝了。  (Usually is 喝水. 把水喝了 has a special nuance. )
  
  你是不是把水喝了？
  
  我开车去上海。  
  
  你是不是开车去上海？
  
  学校离我的家不远。
  
  学校离你的家远不远？  (This is perhaps the best example in these sentences where V-not-V structure is most suitable. However, 远 is a adjective, not a verb... )


By the way, some of the sentences in @fefe's answer are not natural to my ears. I don't know if they are from a different part of China or something.

Basically the part you repeat is the part you want to ask about. So, if you repeat the preposition, you ask about the preposition (usually about place, time, direction, etc). If you repeat the verb, you ask about the action. 

If you want to ask about the whole statement without emphasis on either preposition or action, a generic question uses 是不是, like I said above: 你是不是在中国工作？ Or use 吗: 你在中国工作吗？