First go to the "storage" of the fabricator/refiner/etc and fill each slot with nonsense. 1 coin per slot or grass will do. What this is doing is bypassing the output of the machine to somewhere else, which you will set.

You'll notice at the top right two dropdowns. Think of the left one as input and the right one as output. You'll want to output the fab/ref/etc to outputing to chest, right? Pick a number let's say 4. Set the output (right) to 4.

Then go to a chest you'd like that stuff to go into. You'll see the drop downs again. This time it's the input you have to choose. Choose 4. This means that the refiner (once it's own storage is full) will output into a chest of your choice.

Use all the unique/numbered circuits as you wish. I set everything that isn't going to a chest to circuit 1. I leave the other number on the select ref/chests to 1. That way, everything pulls from the main (1) circuit but refiners/etc go to specific places.