Many doctors learnt by the books and watched dissections happen. Also there was licensing for doctors from new medical school. At these schools they debated the best treatments for disease.
Observation
Some doctors followed Hippocrates' methods of observation. Doctors may check a patients pulse or taste their patients urine to see what's wrong with them.
What was in a doctors toolkit?
The vadmecum diagnosis book
leeches for balancing humours
posies and other high smelling objects to get rid of miasma
herbs for mixing natural remedies
zodiac chart to predict illnesses and suggest cures