The Pox, Draughts, and Amputations
Well In general, surgeons were rarely able to actually effect any real treatment for disease during this period of history. Communicability was understood, in a way, and surgeons could minimize infection, and in general act as "health inspectors" in most cases, to insure that the likelihood of disease was at least averted, as it was understood to occur. The relationship between vitamin C and scurvy was understood, and spruce beer and oranges, limes or cabbage were valued, Aboard ship, the most useful application of the surgeon was in actual surgery.
The Duties of the Surgeon
;From - The Sea-Man's Vade Mecum, 1707 (french)
Medicine - Virtual Naval Archives
This is an excellent source for a general description of surgeons of the time, and their duties. As such, they varied little from country to country. Most required some form of certification, though did not require that a surgeon actually be a doctor.  In fact, to have an actual doctor as a ship's surgeon was rare indeed.
In general, it was suggested that The Owners provided the Surgeons Chest and it's contents. In the British Navy, the Surgeon was given an allowance to provide these items himself. Chests found wanting in supplies in the French navy, when inspected, resulted in fines for the surgeon. One wonders how well the french seamen were able to actually comply with ideas and suggestions such as, " In every Ship, even in the Fishing-Ships, making long Voyages, there shall be one or two Surgeons, according to the Circumstances of the Voyages and Number of the Persons. " Considering the shortage of real medical knowledge, we can understand why most "surgeons" were little above 'barber surgeons".  The requirement was that a french surgeon was tested and certified by two other surgeons. These certificates were required.
The Surgeon was responsible for notifying the officers of any sickness that may arise, and suggest appropriate actions to be taken, and should not accept payment for services they provide to seamen aboard, nor could a surgeon leave the vessel before the end of a voyage.
Examination- After examination, theory at the time considered the symptoms to be the disease, and one treated the symptoms. There were three levels of causes for sickness.
Antecedent Causes;
There were two kinds of "airbourne factors".  Miasmas were disease causing particles that came from decaying matter. The sources were privies, swamps, rotting corpses. Contagions (effluvia) were also invisible particles, but came from other sick people. Although the actual bacterial causes were unknown, at least a move in the direction of sanitation was beginning.
Predisposing Causes;
These causes were both intelligent, and strange, by modern  standards. One needed to consider in what weather and season an illness was incurred.  Also, by being a certain body type, sex, age, inherited trait, or occupation, one would be predisposed to contract certain disease
The Six Non-Naturals;
These would be any disturbances        in the air, the kinds of food or drink, the amount of food, the sleep habits, the exercise habits, and the mental state of the patient. On ship this is not as far fetched as it may sound, considering the likelihood of food to spoil, and the superstitious nature of the century
Treatment-Illnesses were described as "imbalances" of the body, and to treat them, the body had to be placed back in balance. Based on the greek theory of keeping the four humors in balance, if the pulse raced and a fever existed, drugs or food that would cause the opposite effect would solve the problem. In other words. If one was constipated you received a purgative. Then again, you might get a purgative to reduce a fever, or a blood letting, to weaken that rapid pulse.

This theory was reinforced by the 1690's by the solidist theory that nerves and blood vessels were hollow tubes, and health resulted when everything was able to flow freely. If you had a fever, it was due to arterial irritability. Treatment for a fever might include narcotics to remove noxious factors in the body, and to calm hyperactive fibers. Avoiding red meat and other food would prevent the feeding of the internal fires, and bleeding to reduce tension in the arteries.
Common curative measures; Olive oil, as ever before, was a favorite treatment for burns. Wounds were kept clean, and it was known that doing so would allow the patient to recover, though the relationship between bacteria and pus and infection itself was completely unknown. Most salves were made from lard or butter. Bleeding to death after a wound was far more likely, and the method of treatment was to apply tourniquets, or pressure bandages. Drugs were indeed applied, but in many cases these were applied because of their maker's claims, not due to any proven actual effect.
Preventative Measures- On of the largest (or at least most commonly heard of) was the use of vegetables and fruits to prevent the onset of scurvy. Try here for a detailed account ofJames Cook and the Introduction of Lime Juice in the British  Navy
Surgery- Simple fractures and dislocations could be reduced and splinted, but compound fractures and open wounds usually resulted in gangrene. Amputation of the thigh, for example, did not really become a viable option until 1800. General anesthesia did not exist until 1846. Rum or opium were options for making the patient senseless, but in general, fellow crew member's would strap them into place and hold them down, as surgery was performed over a sea chest. Shock itself was welcome, since t relaxed the patient's tense muscles. Amputations were common, but not until after 1800 could one hope to have such an operation occur quickly (two minutes) and shock and loss of blood could account for more        deaths from amputation than the gangrene afterwards.
We did recently receive this comment through the email newsletters, regarding amputations and anesthetics...
The best description of a leg amputation I've read is in John Woodall's  The Surgeon's Mate published in about 1604-1610.  That book is, of course, about barber-surgeons afloat. Everything I've read says that:
Rum was not available (invented? created?) in the 16th century nor was opium available outside of Asia, I believe; Anesthetics were not provided before an operation (too many people never woke up after becoming unconscious so they were kept awake); in all, I don't have anything that shows pain-killers (ale, herbs, etc.) being used during [1500s].

The shipboard [surgeon]--more for general morale in close quarters than for the patient -- used a bowl or bowl-like helm upon the patient's head and a carpenter's (wooden?) mallet to stun the "victim" into being quiet and to being a bit more cooperative. A few surgeons (mostly on the continent) were starting to become enamored with the idea of killing the pain before they operated, but I think part of it was that the pain to be killed was supposed to be of the illness or injury and not inflicted by the medical personnel.

I do know about the sewing together of skin flaps  , a new and somewhat "radical" idea countering the long-time accepted practice of cautery. This was touted by French surgeons as less painful after the "cut", but most other writings I've read indicate that it was just more efficient (cleaner, more apt to heal, etc.). Ligature (clamping off of the major vessels and arteries before the amputation) and sewing were both coming into play by the end of the 16th century as opposed, again, to using the hot iron.[ to cauterize the wound  
   
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- Elizabethan reenactor Michael Foster