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Ender IO can be installed in 2 different ways: Monolithic or modular.
In a monolithic installation you will have most of its content in one mod, called "Ender IO" and a couple of addons you can install in addition. This is how most players will use it.
In a modular installation you leave out that "all-in-one" mod and install only those components you want. The same addons can be added here, too. This is intended for modpack makers.
Here's an overview of what is what: