Note: the Automatic Crafting Table, just like the Project Table, doesn't function like a normal crafting table in terms of Shift-clicking.
The crafting table can also be used as a vanilla crafting table, and is useful because you can put some of the items in and come back later with the ingredients not popping out of the table. The crafting table will provide newly crafted items so long as it is supplied with ingredients.
Advanced Wooden Transport Pipes will not extract the crafted item, so be sure to use plain wood pipe. A Wooden Pipe connected to the table can then, when being powered by an engine, extract the newly crafted item.
Next, a pipe leading to the Automatic Crafting Table should provide the items necessary to the recipe. For example, to have a table automatically craft Wood Pickaxe, leave 3 wood and 2 sticks on the table in the normal T pattern.
To start the automated crafting, a template recipe should be placed on the crafting table.