[indypartridge]

Is it normal for there to be pollen and nectar above or below the brood, or are they normally most of a frame?

Yes, it's normal for there to be pollen/nectar above the brood, and it's normal for there to be entire frames of nectar/pollen.

Do drone cells tend to be consolidated on one frame or scattered amongst the broodnest? How many drone cells is normal?

Depends and depends. When using foundation, I've found drone cells to be scattered around. When foundationless, it seems that drone cells are grouped somewhat. As for how many, depends on the season - more in the spring, less as the summer goes on.

Are queen cups always located at the bottom of the frame, and if so, does that also mean that any filled cups are swarm cells?

Queen cups can be anywhere, swarm cells usually hang from the bottom of frames. A filled cup means they are making a new queen, either for supercedure or to swarm.

Keep in mind that for all these things, there is a great deal of variability. While "normal" may happen more often than not, deviations don't necessarily mean "anomoly".