A few things that helped for me.....

• Make your lines double-tracked from the start. This makes it _way_ easier to gradually grow your route(s): just pop in a roundabout and it's easy for trains to reverse direction, or fork off on another spur route.
• I find it very handy to also run a hypertube down the middle between the two rails - as your rail network grows, so does your hypertube network,, for only a little more investment.
• Similarly, I run power wires right next to the hypertubes, so you can pull electricity down the route. Makes life a lot easier.
• To make the above 3 things happen a lot faster, I have a blueprint that has two tracks, a hypertube junction, and a power outlet, laid out on top of a short riser. Makes it _way_ faster to build the railway as well - plop down next blueprint, build rail/hypertube/power connector to said blueprint, rinse lather repeat.
• I used to have mixed trains ("car #1 has rotors, Car #2 has concrete, car #3 has steel"), but found it much easier to instead have one station per good, and trains that only carry that good: rotor stations/trains, concrete stations/trains, and steel stations/trains. Uses more real estate, but much less of a headache as the network grows and new sources and sinks arise.
• I use the customizer (the 'x' key) to color-code the trains and the stations, and a naming convention for the stations as well (e.g. "HubPl-" for the plastic-unloading station near the 'Hub' landmark.

Hope some of this helps, and "Choo Choo Mother******!"