Unlike IndustrialCraft 2's Electric Furnace, the Automatic E-Furnace has two inputs and two outputs. Additionally, it can not use upgrades like the Overclocker Upgrade, at least in the same way. You must right-click the machine with the upgrade in hand to apply it, and the upgrades CANNOT be removed, even with a Wrench.
The Automatic E-Furnace also includes new configuration in the form of buttons, the left-bottom corner of the GUI. The button that looks like a lightning bolt, when turned on, allows the Automatic E-Furnace to transfer EU to machines next to it, assuming the machine is not using any of the energy. The second button, which has an arrow on it, when turned on, makes the Automatic E-Furnace output through the back of the machine. If an inventory, such as a Chest, is behind it, then it will place the items in the inventory. If not, it simply throw the items on the ground. The last button changes the way items are moved into the output slots.