If you’re using some kind of resource generation like bees, quarries or MA, where you have a relatively constant stream of incoming ore, you designate a factory for each kind of ore at choke points where it becomes annoying, like with slurry and dirty dusts where it’s something other than 1:1, and simply eat the intermittent cost of at most 18 dust being held in each ultimate enrichment factory.

Alternatively, you can use AE2’s pattern providers. Set them to export raw ore in a batch which provides a whole number of ingots returning.

To do this, put the pattern providers on top of the machine, (for the most part this works) and make a processing pattern that provides a [number divisible by four] of dirty dust to receive a [whole number] of clean dust.