Layers is the term used to define different channels of the same server. You are not able to select which layer you are on, however you are able to sync to the same layers with your party members.
For example you can be on the server Green Fluff with your friends. You ask all your friends to meet up with you at Barton Town. The picture below would be a depiction of the minimap you see, and the dots are the players.
You see their dots on the map marking your friends but you do not see anyone standing there. This is because they are on a different layer.
Layers are not parallel with each other. Meaning, if a special event started on one layer, it does not mean that same event has started on another layer of the same server. For example, if you hear someone say there's a Landshark on the server Green Fluff, that does not mean there will be a Landshark on every layer for the server Green Fluff.
The only way to be able to join a particular layer, is to have the person that is on that layer invite you to their crew. When you join the crew you'll notice your game screen transitioning with a closing circle as if you were changing areas, which in fact you are changing layers. If there is no transition then you are on the same layer as the person inviting you to their crew. Another way to change layers is to use a technique called warping. If you have a friend in the same area as you, they would appear on the map as a blue dot. But if they are on a different layer, then the dot would be a lighter blue with an arrow next to it. If you click on the dot, then you will be moved into the same screen as the player, and you will also now be in the same layer as them. This is called warping.
Warning: When you warp to a player, you will not be warped to the same spot, just the same screen. In other words, there is no telling where on the screen you will end up.