If you have two batteries with different voltages, let's say 12 and 9 V, and you connect the negative terminals while you put a LED or whatever between the positive terminals, there will be current flow. I reason that is because there is a potential difference even though both terminals are positive. However, I'm not sure I understand how electron current would work here. 

If there is current then that must mean that electrons actually flow out of the lower positive terminal into the higher one? Is that what's going on? If not, could someone clarify it?