All ponies start with 1 Physical rank. The Physical skill is used for physical tasks and ponies take on a primary and may take on a secondary Specialization. The physical rank is shared between both, but it is assumed the secondary specialization is more difficult for the pony.
Tasks outside a pony's specializations have a score of the pony's physical rank -2. So if a Rank 1 pony with primary Martial skill and Secondary Subtlety skills tries to intimidate someone (typically a Presence skill), they're physical rank is considered -1: They are really bad at this. That same pony at rank 5 trying to intimidate someone would be at 3: They are okay at it.
The ranks are not used for actual 'checks': see rule #3. The idea behind the specializations is to instead encourage players to limit the skills a pony will have and encourage players to find limitations and allow their characters to have failures and flaws. The pony is granted an allowance to be good at something in particular, and encouraged to fail at others.
Martial ponies are warriors. They train in a specific martial art, usually specializing in one particular weapon or art form.
Manual Labor ponies are good at hard, 'unskilled' work. This includes pulling carts, lifting objects, pushing objects, and many common 'chores.' They often have high endurance.
Skilled Laborers are ponies like Blacksmiths, potters, artists or other craftsponies who work with their bodies in careers which require some training and familiarity to master. They are capable of great precision when performing acts related to their skill and training.
Subtle ponies are sneaky or agile, and their physical skills work to this advantage. They may be dextrous and quick, but lack endurance.
Ponies with presence are charismatic or intimidating. Maybe they are bulky and scary, or sleek and good looking. They are versed in body language and generally extroverted.
Performance ponies are good at performance arts, like Dancing, Public Speaking, or Acting. They tend to have good physical memory and an excellent spatial awareness of their body to their surroundings.