It's easy to research where the trade routes were for any given period of time. I wanted to know where goods were exchanged. Specifically, how organized was this process? Did all villages on the trade routes have markets and all of the exchanges took place there? Was it more of an exchange of goods, or was there a common currency (eg: gold)? Did the end-user purchase the item directly from the traders who traveled on the trade routes, or were there just as many middlemen as exist today?
If someone could point me to any references about how trade historically took place, I would also love to read it!
It depends on what type and scale of trade you are talking about. Some types of trade aren't really done from a profit motive, and are more accurately termed "exchange". A classic example is the so-called "Kula Ring" famously described by early anthropologist Branislow Malinowski, in which the Trobriand Islanders would exchange items to partners who are well known and for reasons of cementing personal bonds rather than gaining economic advantage. Lest we think this is something only weird islanders do, think of Christmas or other gift exchange holidays, in which items are exchanged personally from face to face interaction.
But if you mean in terms of economic exchange from profit motives, historically this has frequently been done at set market times or fairs. Peddlers, for example, would typically travel a set route corresponding to different market centers, For example, in a workshop in Pompeii the owner had scratched on the wall plaster the schedule for the market fairs in the towns in the surrounding region. This person would thus be able to travel to nearby towns in the knowledge that when he arrives there he could sell his wares from some sort of ephemeral stand.
What you are really interested in, I suspect is more large scale affairs. For example, I study the trade between India and Rome, which was largely carried out on large ships travelling between the Roman Egyptian ports on the Red Sea and the ports along south India. We know from literary sources that these ships would make frequent stops along the way and engage in "tramp trading" in smaller ports along the way. How did this work? From comparative evidence it is likely that the members of these villages, which would frequently be fishing dependent, would simply sail or row out to meet the larger trading vessel (which could not approach the coast) and engage in barter in that way. They might carry, for example, a load of food or water supplies and exchange it for wine.
How the trade was conducted when the ship reached its destination is a bit murky. The traditional view, still somewhat bafflingly supported by some scholars like Whitaker, is that the trade was entirely within the hands of "princes", that is the local rulers who engaged in it purely to obtain high prestige items. This has no support, but it is likely that local authorities were involved in organizing trade in some way. For example, at the Gujarati port of Barygaza it is said that local ships would go out to help guide the Roman vessels through the shoals, and goods would be led up to a warehouse to be stored before being sold. It is quite likely that these goods would be sold at an auction or through some sort of dealing between merchants. Facilitating this would be Roman merchants who resided year round in India.
All of these large networks (such as the "Silk Road") were really groups of middlemen, depending on your point of view. A glass bowl travels from Italy to China through innumerable different hands by being absorbed into preexisting trade routes.