In the eighteenth century (as well as into the nineteenth century), medical education - that is, to become a physician - was generally restricted to wealthy white men who would pursue learning at a limited number of institutions renowned for medical education in particular. Typically, classes would take place in a rounded lecture theatre, where a professor would teach while a surgeon dissected whatever part of the cadaver was relevant that day. Notice the distinction between the professor and the surgeon - this existed just as strongly in the medical profession. Doctors held a certain amount of status, but surgery was considered dirty and barbarous work, and was typically conducted by someone of considerably less status (often even by barbers).

Medical education, and the profession in general, was not heavily specialized as it is today (e.g., you would not find many gastroenterologists, obstetricians, or cardiologists). People were just doctors - specialization came about during the early- to mid-nineteenth century and has been growing ever since.

One of the biggest problems in medical education was amassing the number of cadavers needed to allow detailed anatomical learning and practice for the medical students - schools were almost always short on bodies. This led to some very interesting and horrific practices in a number of schools, especially in the southern United States (see Harriet Washington's Medical Apartheid) that involved an uncanny amount of grave robbing.

As such, medical knowledge was severely limited and maintained its ties to (literally) ancient ideas about the nature of disease. Many doctors still subscribed heavily to humoral theory, which is essentially the idea that people contain four essential substances (phlegm, blood, black bile, and yellow bile) and that an imbalance in the levels of a certain substance was the primary cause of illness. We can still see the influence of these ideas today, particularly in "temperament personality tests" that you may have taken yourself. Still other physicians attributed epidemics to miasma; this was essentially a noxious smelling or contaminated air which, when breathed in, caused illness. This was the case for Benjamin Rush during the infamous Philadelphia yellow fever outbreak of 1793; if you're interested in learning more about medical knowledge during Jefferson's lifetime, reading Rush's journals and books about this outbreak would be the perfect place to start.