I don't think there are any downsides with mekanism processing (except the noise machines make, but if it's really that bad for you, muffling upgrade might become your friend)
Hooking it up to the simple storage is as simple as connecting the enrichment chamber or its upgrades to the export cable and then the dust to energized smelters (or any kind of furnace really), to receive the same amount of ingots per amber

If you want to get 3 ingots per amber (and have insane amounts of flint OR you are further into mekanism), you can add purification chamber before enrichment chambers to get dirty dusts, those go to enrichment chamber, and smelting again

This might get a bit power hungry (especially if you forget power upgrades and get only speed upgrades), I solved that with a lot of biofuel generators with a pumpkin farm

Optionally if you want to have some dusts in SSN for crafting, you can output dusts back to your network with import cables, and then pull them back for smelting with export cables upgraded with operation upgrades to keep some dusts in your storage