What is the difference between queen cells and "emergency" queen cells, and what makes the bees decide what type of queen cells they make?
Queen cells are the same, its the intent or reason for the cell that helps us dictate the "name" of the queen cell. Swarms cells (usually at the bottom of a frame. hive is going to swarm)
Cell in center (sometimes upper) of frame usually is a supercedure cell (they see a reason to replace/supercede the queen), or emergency cell (queen is no longer present, and must have a queen asap).
If you do searches on queen cells, swarm cells, supercedure or emergency cells, you'll find a wealth of information in the archives on details of each. bushfarms.com is a great place to start.
I accidentally killed a queen in one hive and when I went back a couple weeks later there were emergency cells, they are all over the place, as the colony is desperate for a queen and use whatever brood possible. Fortunately they have kept that queen to present, her name is Spot II. ;)
It just depends why they are making the queen(s) as to where you'll find the cells.