With machine crafting we will need to use the other type of interface, these will need to be stuck onto the machines you wish to autocraft with. It's advisable to have seperate machines for autocrafting and normal crafting, this eliminates any clogging. Interfaces will name themselves when attached to machines, if you have lots of machines then you can name these with name tags.
You will need to set input and outputs for machines when using interfaces.
It's very important to ensure that your machine patterns are correct, if not your system will hang while waiting for an item. Most EnderIO machines have some kind of extra output, for example when processing ore you might get bonus dust. As this bonus dust is not a 100% chance, you will need to ensure that it is not within the processing pattern. If it's not a 100% chance do not add it to the pattern. The same goes with the amount of dust (for example) if you only get 2 dust per ore then ensure you only put 2 dust within the processing pattern, otherwise your system will hang waiting for the 3rd or 4th dust.
Slapping on interfaces to machines and adding the correct crafting pattern will show the crafting recipe within the crafting interface.
Molecular assemblers can also be used on their own, as these only require power and a crafting pattern to work, as long as they are fed items via a hopper or any item carrying pipe.