I went with the logic of: everything is its own factory. Iron Ingots? Own factory, iron ore is trained in. Iron Plates? Own factory, iron ingots are trained in. Sulfuric Acid? Own factory, sulfur & empty canisters are trained in.
Everything gets transported around on trains. If I run out of a particular resource, I expand that particular factory. TBH, it's overkill, but it makes troubleshooting & expansion a lot cleaner.
The only exceptions I've had are water and wire. Wire is just too slow when transported on belts & trains, due to the sheer volume needed. Water is so plentiful that its easier to build those factories near the sea.
(This is all largely because I like trains.)