I have everything feeding directly into my energy condenser and 1 chest with 1 copy of each base component, (dusts, resin, gems etc) that act as my blueprints for swag. So as I need it, I make it. Any left over after production go back into the condenser. I hate chest clutter and like building stuff from sctatch so I wont use the energy condenser to make components or machines as that feels too much like cheating, raw materials only. Keeps it tight for space and saves getting chest sickness from all the running/spinning.
If I were to go the chests route tho I'd have a room for the base items and automated crafting each leading into a "workshop" for tech parts and machenery, "garden shed" for outside stuff, a " kitchen" for the food, armor room... that kind of thing. All rooms big enough to store ample finished product whilst keeping them seperate and easy to find.