To Answer a few questions:
I would appreciate any help as I plan to do a split soon on another wintered through hive. Perhaps if I let them make their own queen the stock would be better?
hives will often make queen cells on different frames, using one of those frames with queen cells intact to start a nuc (which is actually a split but with smaller numbers) and gives the nuc a queen relatively soon. Then if the supercedure in the parent hive has failed for any reason the nuc can be recombined using the newspaper method.
As far as making better stock, that is a subject of long, and often hot, debate. It is what the bees do naturally so it can't be all bad. My experience that your just as likely to get a good queen by supercedure as by buying a queen, but then the reverse is also true.
On one of the frames I noticed that there were three huge cells toward the top of frame.
One was capped, one was mostly capped and had a huge larvae in it and the last one was empty.
That is not unusual. The bees will have the queen lay in different queen cells on different days as backup insurance, the problem with it is that with staggarded queen cells the hatch of the second days after the first can induce a swarm when one isn't wanted by either the beekeeper or the bees. Another reason for moving a frame with queen cells out of the hive temporarily if on sparate frames. If on the same frame once cell can be carefully excised from the combs and pressed into the combs of another frame of brood that can be used to start a nuc.
How is it they are empty, a queen hatched or do they build these queen cells first.
A beekeeper will often enter a hive and find as many as a dozen queen cups--started but unfinished queen cells. These are there as insurance. some hives have queen cups all year, they make some, tear them down, make some more somewhere else, etc.
I had thought they made a queen out of a worker egg laid in a regular worker sized cell and proceeded from there, but it sounds like they also make these large empty cells. Am I understanding that correctly?
They will do that in an emergency, such as when a queen is killed while manipulating the hive. But if a swarm or supercedure is by design so is the queen cells. The workers will build the queen cells, or build up the queen cups, and then force the queen to lay in one or more of them.
As a general rule queen cells near the top of a frame denote supercedure, queen cells along the bottoms and ends of the frame will indicate swarming, and a few cells found at random wherever is an emergency queen. The emergency queen is indicative of what was asked, altering a worker cell into a queen cell.
Does the queen generallly lay alot more drones in one area or would she just lay 3 there?
Is drone larvae and queen larvae the same size?
Drone cells are usually grouped together and found on a separate frame or the parts of the comb closest to the end bars. Drone cells look like a .32 cal bullet sticking up from the comb. Queen cells look more like peanut shells. All eggs and larvae are the same size, the change takes place during the pupae stage.