I cannot give you a very comprehensive answer for all trading companies, but I can give you a short explanation regarding the Dutch United East Indian Trading Company: De Vereenigde Oostindische Compagnie (from now on VOC). Note that the system of the VOC was much intertwined with the gouvernment of the Dutch Republic, and that it had a quite complex organizational structure, that evolved and changed here and there during the two centuries the VOC existed. What follows is a brief summary of the history of the VOC and its organisation.

The VOC was founded on the initiative of the Dutch Estates General (form now on Staten Generaal), the governmental body of the Dutch Republic, impersonated by the state pensionary Johan van Oldebarnevelt. He insisted that the various trading companies that were founded shortly after the first Dutch journey to the East Indies returned successfully, joined together. As a united company, he reckoned, they would stand a better chance against other trading companies. The profit form such an undertaking would bring in the financial means to wage war against Spain (the 80-years war), and on the same moment hinder Spanish endeavors in the East Indies. So in 1602 the VOC was founded, with heavy state influences.

Like the Dutch Republic itself, the company had no CEO or something like that. The board of directors was formed by seventeen men, the Lords XVII from the aristocratic class of regents, wealthy civilians with often direct connections to the Staten Generaal, the Provincial States, or other governmental bodies in the country. This made the VOC extremely influential in Dutch politics and the difference between the VOC and the government of the Republic is sometimes quite vague.

The 'management' was divided in six different offices, 'rooms', spread out through the Republic. Each room delivered a number of deputies to the Lords XVII according to the financial input said room delivered to the company as a whole and the number of assignments a room had to do. The council of the Lords XVII decided on what goods should be bought in the indies, in both quantities and qualities and set the outlines for how much money could be spend and how much profit could be paid to shareholders. With those instructions each room had to outfit its own ships and crews to meet these assignments made by the Lords XVII. The boards of the different rooms were formed by regents, members of the aristocratic/merchant class. Within those rooms, different commissions were formed to carry out the different tasks each room had. Every room had its own shipyards, stockpiles of supplies, stocks of trading goods and anything else to maintain daily business.

A major part of the power of the VOC laid not only in the huge amount of money the VOC brought in. Like I said before, the goal of the VOC was to earn as much money as possible to finance the war against Spain and to do so, the Staten Generaal declared that the VOC had the monopoly on the spice trade with the East-Indies. To protect that monopoly, the VOC was given a huge mandate to do anything it could to maintain its monopoly. The VOC could wage war, forge alliances and therefore was a considerable political body. Lines between the navy and the VOC were short and sometimes the navy supported the wars the VOC waged in the far east, while when the Republic got into one of its many wars with England, the admiralities of the navy requisitioned the armed merchant ships from the VOC as an auxiliary force.

In the factories and colonies in the East, the VOC had something like a CEO: the gouvernor-general. He represented the Lords XVII in the far east and had an extensive office with lots of clerks working in Batavia (nowadays Jakarta). He was supported by the High Council, which had to approve the decisions of the gouvernor-general. Without each other, the council and the gouvernor-general could not rule. Other factories and trading posts, like Dejima in Japan, had gouvernors of their own, who were subordinates to the gouvernor-general in Batavia. The gouvernor-general, however powerful, was subordinate to the Lords XVII back home in the Republic.

It's also interesting to take a look at the situation on board of a ship. A fully equipped retour-ship (a ship purposely designed to travel between Europe and the East Indies, as far as Japan), could have a crew of around 300 men, including marines. The most important rank was not -as one would probably expect- the skipper (captain), but the chief merchant (koopman). He was responsible for the ships finances. It was his responsibility to make sure that the journey was profitable: that the crew received its salary, that goods were sold for a good price, and that goods were bought for as less money as possible. It was the chief-merchant who decided on many things on board, such as do we anchor in this port to restock on supplies, or do we save money by cutting rations for the crew and sail on to our destination as soon as possible? Together with the skipper, he would report to the gouvernor-general in Batavia, or to the Lords XVII in Amsterdam on arrival in port, with an extensive cash balance of the journey and a detailed log of the entire journey.

Finances for these journeys were not only brought in by profits form previous endeavours, but mainly from trade within Asia. While the long journeys between Europe and Asia were very expensive and the holds of the ships were relatively small, most of these were barely profitable and during much of its existence the VOC was on the brink of bankruptcy. This was masked however, by the profits from trade within Asia and the profits made by selling shares on the stock market. This was also done when the VOC was founded. Shares were mostly bought by rich entrepreneurs and regents, but there is evidence that more ordinary people also bought shares in the VOC.

If you want to go deeper into the history of the VOC, you can take a look into the archives of the VOC. The Dutch National archives has more than a kilometer of archives from the VOC, which is almost completely accessible online. The archive of the VOC ranges from maps and drawings to journals from voyages and cash books. See https://www.nationaalarchief.nl/en for more information.

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