When you install CER, it won’t do anything at all until you create at least one preset. A preset is a relationship between two reference field instances, which are referred to as the left and right fields, respectively. When a change occurs in the left field, the right field will react — and vice-versa.
An example: suppose you have a user reference field called Author, and it lives on Page nodes. You also have a node reference field called My Pages, and it lives on users. You can set up a preset that looks like this:
Node: Page: Author <--> User: My Pages
In this case, Author is the left field and My Pages is the right field. When the Author field is changed on a Page node, the referenced user(s) will be given a back-reference to that node.
By default, presets are bidirectional. This means that a change on either side of the preset will affect the other side. The previous example is bidirectional: you can change Author or My Pages, and the other side will react accordingly.
It's possible to make a preset one-directional, which means that the right side will react when the left side changes, but NOT the other way around. In a one-directional preset, changes to the right field will have no effect on the left field.
A one-directional version of the above example would look like this:
Node: Page: Author —> User: My Pages
So what this means is that, in a bidirectional preset, it really doesn't matter which field is the left one and which is the right one. They’ll affect each other equally. But in a one-directional preset, it does matter which side you're on. CER allows you to "invert" (flip) a one-directional preset.
Internally, CER treats all reference-type fields the same way, which allows you to put a different kind of field on either side of a preset. You don't have to necessarily relate a node reference field to another node reference field. You could relate a node reference field to a user reference field. The only restriction is that each side of the preset must be able to reference the other side. So, to again use our example, Author needs to be able to reference users, and My Pages needs to be able to reference nodes (of the Page type). CER won't let you create relationships between fields that can’t actually relate.
CER presets are entities built on top of Entity API, and they can be imported and exported just like any other exportable entity type, including support for Features.