To gain the benefits of a rare resource, a Merchant needs to deploy next to it, thereby turning itself into a small "building" (it remains a unit, though, and takes damage like the mobile Merchant unit). Only one Merchant unit per nation is allowed to harvest a particular resource location. However, each nation may deploy its own Merchant next to a resource. Sending Merchants to rare resources located in friendly/allied territory is a common strategy.
The Merchant unit may also pack itself again and move on to another resource. This might be useful, if the current resource lands in enemy territory and the Merchant unit starts to take attrition damage from it. Note that Supply technologies prevents attrition damage in enemy territory while deployed for Merchants, since they are not moving.
The Dutch train Armed Merchant instead of Merchant, which is equipped with a light weapon to provide basic defense against raiding attacks. However, the Armed Merchant will cease to provide its bonus while attacking.
The game files show an unused Merchant icon possibly intended for the Gunpowder Age and the Enlightenment Age, as is the case with most civilian and support units. It is unknown why the icon ended up being unused in-game.
Amusingly, the icon bears a striking resemblance to Juan Valdez.