MATTHEW,
First of all, it is best to unite a strong or medium hive with a weak one.
The newer or better queen should be on top in one deep.  I tried to winter
with excluders and ended up with one colony up top, lower queens abandoned.
This is due to heat rising and making the upper unit more smelling of
pheromones, so you have a drifting to the top with every winter flight.
I use 7/8" augur holes in all supers. With three deeps, you can close the
lower hole, and leave the upper 2 open. With 2, both are open.  Bottom
entrance is reduced to 2x.25" with a wooden cleat.  All entrances are on the
south or SE side.  You can use a regular inner cover screened one side.
Better is an inner cover with a bee space on both sides to allow for feeding
pollen supplements every 7-10 days when it's above 35°.  They eat up to 36
oz. of patty per week!  This way you can make honey on early flows, as well
as late ones, and lots of divisions, provided you keep 2 queens all summer.
Mostly, supers are filled between the units, but you may need 3 excluders,
to keep the queens out of the supers if used above the top brood chamber.
If you are rugged you can keep adding supers between the units, but I like
to put the heavy ones on top, for removal, and so I don’t have to lift the
3rd deep so high.  A deep or two shallows will hold them for a week usually,
except on a very heavy flow, like we’re having now on Japanese or Mexican
bamboo (Polygonum cuspidatum.)  I’ve recorded 15 and 16 pound gains in 24
hours.  It’s amazing how they can gain a half pound in 2 minutes around 5
PM!
Charley