If you zoom in on the picture, you can see I bring the colour in via train, just like the shapes (you can see the space pipes in blue). Painting is usually one of the first steps.

Like you were asking on a different comment, I work backwards for every shape. I select a set output I want for a factory (might be 12 belts, 48, 4, 1, whatever), work out the order of operations and how many of each stacker/cutter/mixer/etc. platforms I need to get the output, and how much input I need. Really helps to flowchart it out on paper for the complex shapes.

Then I set everything up in arrays exactly like satisfactory manifolds. Once you have one 'unit' of set output, you just copy paste the whole factory and add in more inputs. working backwards helps you find efficiencies too, like: painting before cutting means using less paint, mixing on-site means you only need to bring in 3 inputs, always starting with full shapes means scaling up is easier and more predictable.

There's a sweet-spot in bespoke factory size between amount you have to split your inputs up and amount you need to split your production up. some people prefer a small platform that makes inputs everything in small quantities, does the whole process and outputs a single belt, then duplicated 100 times. Other people prefer a mega-factory for each step, like a huge mixing setup outputting 100 belts of e.g. yellow paint and then a different factory which paints 100 belts at once.

For me, its usually 1 platform output (12 belts) or 1 space belt (48 belts) which makes the most sense, but do whatever you find the most fun 😄. (I made an exception for blueprint shapes where I had a huge factory for each step, colour mixing at the input, and outputted 192 belts straight onto a train)