The ME Pattern terminal has two modes it toggles between. In "crafting bench" mode, you create a crafting pattern using the 3x3 grid and it detects the output, and the programmed recipe can go into an interface next to a Molecular assembler.
In the "Furnace" mode, you put the items into the 3x3 grid, but the shape isn't important. You manually put the output from the recipe in the 3 slots on the right. This programmed recipe can be placed in an interface adjacent to a Furnace / Induction Smelter / Grinder / whatever it is that actually makes the recipe. So you can create a recipe that associates "Iron Ore" with "2x Pulverized Iron" and drop it into an interface next to a TE Pulverizer. The interface, when ME is asked to craft pulverized iron, will inject the ore into the adjacent machine, but it will not auto extract the output - EIO can push back, but TE machines generally cannot accept from, and push items to, the same side, so you need to hook up some itemduct to carry the product from the output of the Pulverizer, back into an interface - pushing items into an interface signals ME that the craft is done.
An interface only pushes into one thing, so more complicated recipes can be automated by placing an interface next to a chest, and putting in a recipe that associates Empty Fluxduct and 4 redstone with Redstone Flux duct - and then you use EIO or TE itemducts* to move items from the chests into magmatic furnaces and fluid transposers, and then more itemducts to push the completed items back into the interface.
There is very little that cannot be automated, with some ingenuity, with ME.
* Or, an ME subnetwork.
