Hey former SF4 staff here, check out:
For Mekanism machines you MUST set the side configuration. This includes energy, input, output, extra items such as bi-products (usually purple colored square). Youll also need ME export buses to put the items in the machine, and ME Import buses to take out the produced items. To make this toggle-able through a terminal instead of 24 hour crafting, use an ME Interface, and put the pattern inside.
You may have to do: ME INTERFACE into a Chest, then items in the chest into the machine with import/export buses (or itemducts) then export the product from the machine, straight to the ME if your project is on a larger "line" scale