Chances are, you won't be extracting frames from the bottom as that is where your broodnest is. I've heard of nubeeks extracting brood comb before, it ain't a pretty site.
If all you have is 2 supers per hive you probably shouldn't take any of their honey. What will your bees live on all winter? Please don't say syrup
The clustering outside that you observed could have been nothing more than your bees being too hot and hanging outside to cool off. It may not have been a swarm....although w/ only 2 supers...it can happen even in September.
With the sticks separating supers; that may very well be the case as bees will bring in fresh air and ventilation from the openings we as Beeks provide them.
If you remove "honey" supers now, and there's only 2 supers per hive; Yes your bees will be crowded. They may also be homeless.
"IF" you still end up removing these supers for extraction, clean up can be done either way as joeD described above. As for storing; stack on top of screen and place screen over top of stack in a cool/cold place.
Your questions left me asking more questions.....