Thank you for reaching out with this beekeeping question. You're right that beekeepers overwinter honey bee colonies in different configurations. While it is certainly possible to overwinter colonies in a single deep hive body, it's usually much easier for newer beekeepers in Michigan to overwinter in 2 (or even 3) deep hive body boxes (or the equivalent in medium hive body boxes). 

Wintering colonies in a single deep requires a good understanding of the population size and the amount of food needed, which can be hard to gauge without experience. It also usually requires winter feeding.

Wintering in 2 deeps (or 4 mediums) means that there is a little more leeway in the ratio between population size and amount of honey. Many beekeepers who winter colonies in 2 deeps will need to feed heavy sugary syrup (2 parts sugar to 1 part water) in the fall to make sure the colony has enough stored food. These beekeepers may also provide winter feed (dry sugar, candy board, winter patties, etc.), but it's easier for the colony to access honey or syrup stored in the combs.

The University of Minnesota Bee Lab has taught a wintering system in 3 deeps (or 5 mediums). The nice thing about this system is that when all the frames are drawn and filled, there is normally more than enough honey for the colony to survive the winter. Thus, less experience is needed to know how much food the colony needs to survive, and feeding in the fall may not be needed.

Here is the University of Minnesota Bee Lab's Beekeeping in Northern Climates Manual.

The difference between deep and medium boxes for brood chambers depends on beekeeper preference. Deep boxes are much heavier than medium boxes, especially when they are full of honey. Using medium boxes means you may need to check more frames during an inspection or to find a queen before a split.

Regardless of which configuration you choose, we suggest distinguishing brood boxes (used for the colony year round) from honey supers (used spring through fall to collect honey for humans). Frames/combs in the brood chamber boxes may be subject to contaminants that we don't want in honey for humans, such as varroa mite treatments not approved for use with honey supers, antibiotics, mice nests in the winter, bee poop in the winter, etc.

Happy beekeeping!