In your cities there will be trade, communication, and other economic-like activity, produced and facilitated by rivers, roads, buildings such as banks, and trade agreements between cities. All of this activity is described in the game with the abstract term "Trade," which represents at once the flow of commodities and money, the free exchange of information, the movement of citizens, and other things related to movement.
Trade is used for three things in the game, allocated based on priorities that you set:
Although cities produce individual items of trade, called "trade points," they have influence on an empire-wide basis in the form of taxes and research. Gold from taxes is collected into your imperial treasury, and building maintenance and bribes are paid out from that treasury. Research takes place for the benefit of your society as a whole, not simply for the cities that perform it; the progress made anywhere in your lands improves the welfare of all of your people.
Each turn, you may reallocate the division of your nation's trade between taxes, research, and luxuries. (There is a limit on how much you may spend on any one category, based on your Government Type.) That division is respected in each of your cities as those cities perform their production of trade during the end-of-turn update. Each turn's yield of trade points will be divided into discrete units of gold coins, research points, and luxury points.
The game begins with 50% of trade going to taxes, and 50% to research. You may wish to change that to 60% for research, the maximum allowed by Despotism, since in the early years you have few buildings that need maintenance, and your small populations need no luxuries. As the centuries pass, you will have to watch your treasury, increasing taxes when it drops too low, and increasing luxuries when your cities need the morale boost.
The section on Cities will have more on the economy and its allocation.