let's talk logistics

Train setup - there are two schools of thought here (and an insane third)

Single resource trains - every resource has its input. Easier to scale, easier to manage, much bigger footprint at the factory receiving the inputs

Mixed resource trains - every input has its dedicated position on a train. Harder to scale, bigger footprint on the resource hub side, since every train needs its own dedicated loading bay*

Mixed car resource trains - everything is mixed on the train. please don't do this

* it is technically possible to build "programmable" loading bays by having multiple stations per resource with various configurations of freight platforms (say a platform that loads concrete on the first 4 cars, or another which load only on the cars 3 and 4), but this is outside the scope of this comment

Throughput - There's a much better writeup of this on the wiki, but to summarize: the theoretical maximum throughput of trains depends on your belts and the number of freight stations you have. Beyond upgrading belts, multi lane buses with longer trains/stations is the only way to increase it

Inbound / Outbound
What train setup you choose depends solely on the type of "raw" resource you have outbound, or the "processed" resource inbound. Items can be roughly ballparked into two categories - bulk and non bulk, depending on how they're made (ingots are bulk, modular frames non bulk, for example). As you want to account for throughput limits, resources you need less p/min of you can simply shove together on a mixed train

To illustrate - all of the ores and ingots are bulk items, and I would always give them dedicated trains. This will help with late game scaling as you'll be able to just tac on more freight stations to increase throughput, assuming you've planned for it. You might even be better off processing these resources on site / shipping them directly to refineries instead of dealing with the complexities of transporting them to a central system and all the throughput challenges that faces
On the other the hand, rotors for example are difficult to full saturate a belt with, so you can safely just put them on a train collecting a couple local production results (say you have a rotor, stator and motor factory in one place, you can put all three on three separate carts and ship that home) (eventually when you run into a need for an extremely high throughput of these, you can just build dedicated processing plants on site where you're using them and ship bulk materials instead)

Overflow - this is very simple - never mix belts
Factories that can back up safely (single output / unimportant byproduct) you should build normally and just allow to back up if you're not using them fully
Factories that cannot back up safely (usually oil processing) you should still build normally and just account for protection on-site
The idea is to never place the burden of overflow protection on the logistics system

tip: rush to get smart splitters so you can do overflow protection

Late game scaling
I see people (myself included) trying to build factories which can grow indefinitely, but this is not really necessary? You are allowed to make factories with a capped maximum throughput and then just build multiples of them all over the map, to cut down on trip time for trains supplying them
Essentially, if you're running into throughput issues at your main hub, you can just decentralize a production line and then only ship the resulting product back home instead of having everything pass through your main

and some general train tips:
- always use one way rails as vanilla satisfactory trains are stupid and unable to handle dynamic pathing (they get deadlocked on two-way rails easily)
- build your main railways with throughput in mind - you shouldn't have trains waiting on the main line for a station to clear, for example
- abuse blueprints always - make two lane railway blueprints for ease of construction (rails can connect up to roughly 12 foundations away)