Can you use the well to use an action space that still has cubes on it?
Yes. For example to avoid getting black cubes - if you would ever want to. You find that answer in the FAQ-sec. at the end of the rule-book.
Can you travel to more than one city if you have the resources?
No! It is not expressed in the rules. But since you are allowed to put someone new to travel OR to move one guy which is alredy travelling to an adjecent city it was quite clear for me that you can only travel once per turn.