With Mer-Man I do the same thing as many other folks- the modern head is Mer-Man himself while the alternate vintage head is one of Mer-Man's warriors. Mer-Man's powers can change depending on whether he is under-water and how long it has been since he last submerged. Typically, on land or after brief exploits he is his typical green color, but when residing under water for long periods of time he takes on a lighter bluish color, as his boy is more hydrated by Eternia's seas.
Man-at-Arms simply has a younger version w/o his stache and an older version with his stache.
Teela has her regular unhelmeted head and her helmeted head which she uses in conjunction with her Snake Armor and her staff of Ka. The staff of Ka and Teela's Snake Armor are ancient Preternian Snake Man relics which help to augment the vision of the wearer. By themselves, the Snake Armor is just armor and the staff of Ka is just a staff, but when combined, Teela can see through the eyes of the staff. The staff can function as a periscope or binocular type device, be planted to keep an eye on a certain location, or even be "lost" to an enemy in battle in order to spy on them! The Snake Armor was given to Teela by the Goddess before she faded away, having fulfilled her role of ordaining the newest He-Man, but Teela had to go and recover the Staff of Ka. In order to assume the role of Captain of the Guard, Teela had to choose for herself a challenge and fulfill it: she chose to track down and recover the ancient Staff of Ka.
Battleground Teela is Teela on the run and in disguise. At some point during the era of He-Man, Teela has left her position as Captain of the Guard and set out on her own, unsure if she wants to follow in the footsteps of the Sorceress of Grayskull but also searching for her biological father. Changing her hair color and her appearance, she embarks on a quest to discover if she is strong enough on her own to handle the lonely life of being the next Sorceress of Grayskull.
BA He-Man & PED He-Man are simply He-Man in different armors. There is nothing too special about He-Man's armor except that it provides better protection from certain types of weapons (He-Man is by no means invincible in my canon).
Kronis is Trapjaw before he failed Skeletor and was left to die lacking his jaw and an arm. Skeletor was impressed by Trapjaw's resilience in overcoming his near fatal wounds and kept him around. His green head is a result of disease working its way into his face when Trapjaw installed his new jaw.
I don't have a great explanation for Moss-Man yet. I typically only use his modern head. I've toyed around with the thought of his Beast-Man head as an angry head for Moss-Man, who can change his appearance along with his expressions. Typically a peaceful and stoic being, when Moss-Man or Eternina's natural life is threatened he exposes his savage side.
Whiplash's 200x head is his normal head. I don't really ever use the vintage head, but I guess it would simply be another warrior from Whiplash's species.
Bow w/o his stache is a wandering bard and trick archer who secretly collects information for the Rebellion. After he has been exposed, however, he becomes an outright fighter for the Rebellion, losing the heart and circlet that was part of his performance garb, growing a mustache, and becoming a harder individual who desperately seeks to pierce the heart of all members of the evil Horde with his arrows.