The basic idea behind this is that we give our system patterns that we can then request, these will then be crafted and then in turn put back into our system.
The first thing that is needed is a ME Pattern Terminal, much like a Crafting or a normal ME terminal you can right click to open it. This interface will allow you to create patterns, it will let you create crafting patterns that can be made in the crafting table and you can also make processing patterns that can only be crafted in machines e.g. Iron ore will create Iron Ingot within a furnace. This can be toggled by clicking the little crafting table.
The default crafting terminal will show all of the items within your system, you can also toggle this on the top right to show only items that are craftable, having at least one interface showing craftable items is good to have, this will be empty for now.
This interface may look like a normal crafting terminal but you will not be able to craft anything, you can take items out and start to craft but these are ghost items, these recipes can be encoded onto a Blank Pattern Cell:
Once patterns have been encoded you can edit the pattern by putting them back into the crafting interface, edit the pattern and then click recode. You can see what pattern has been saved within the pattern by holding shift. You can clear the patterns by holding shift and right-clicking with the pattern in hand.
Be very careful and exact about what your pattern is, crafting is usually no problem but once you start making more complex processing patterns you will have to tell the pattern how many of X (1 Iron ore) makes Y (2 Iron dust) otherwise it will not work and it will clog your system because it will expect the wrong items to come out of the craft.
Once you have patterns you will need to put these within interfaces. First we can tackle crafting patterns (like within a workbench) then we can move onto processing patterns. To get autocrafting working you will need 2 main things: a molecular assembler with an interface attached and at least 1 1K crafting Storage.
Each interface can hold up to 9 Pattern Cells. 1 Molecular assembler with 1 interface attached to it will craft 1 item at a time, the interface will give the molecular assembler the items and tell it what to craft with the items provided. You can add up to 6 assemblers to one interface. You should add speed upgrades to each molecular assembler to speed up the crafting.
You must add at least one crafting storage to your system, crafting monitors can also be used to see what is currently being crafted. A cluster of these Crafting Storages is called a crafting CPU.
Once you have attached your interface and your assembler to the network you will be able to see whatever crafting patterns you have added to the interface in your crafting interface. You can sort your system by what is craftable, once you have added at least one crafting storage, one interface (don't forget speed card) and one molecular assembler you can start the craft.