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This may seem like a waste of trains, if they spend a bunch of time idling, but having them sit there doing nothing costs you nothing. Trying to be "efficient" by making one train do multiple types of deliveries (i.e. iron+copper) can be tempting, but it greatly increases the risk of creating headaches to sort out.
A slight bump up in complexity is to give all identical stations the same exact name and dynamically set their train limits. For example, you've got one iron mine that's drying up, so you expand to a second one. How do you get the iron ore delivery train to choose the right station to go to? Well, if they've both got the same name, like "iron ore supply", a train set to go to a station of that name can go to either station.
By default, a train will try to go to the closest correctly named station (as far as its pathing is concerned). While that's not usually a bad thing, it can be less than ideal. So, you can wire up the buffer chests to a combinator, wire that to the station, and have the output of the combinator adjust the station's train limit based on the contents of the buffer chests. Done correctly, this allows the station to "tell" a train if it is ready to receive a train, and one station isn't but another is, the train will go to the station that is ready.
*Some exceptions exist. For example, you might want an ore train at a mine's station to "wait until full" OR "until inactive for x seconds." That'll allow the train picking up the last of the mine's resources to move on without manual input.
Are you confident with rail signals? If not check this https://youtube.com/watch?v=DG4oD4iGVoY
What is your end goal? Launch a rocket? Build a mega base? You have to plan based on that. What people usually do is when main bus design is not good enough anymore, they build separate factories connected with trains, where each factory produces only limited set of resources. Trains allow you to put enough space between factories so you can scale them almost infinitely. Trains also make expansion easy. Need new juicy ore patch? Just build tracks to it, connect it to your network, name the station, set the train limit with circuit based on amount of ore in boxes. 5 minutes later your problem with ore is gone.
https://www.youtube.com/watch?v=3TKBs6TD7WU&list=PLV3rF--heRVu2xlDGZiRbdb7nbwzM9Vyz
There are more in his playlist:
https://www.youtube.com/playlist?list=PLV3rF--heRVu2xlDGZiRbdb7nbwzM9Vyz
Oof not sure even that dude understands how they work judging by where hes putting signals, as mentioned by Helmey112 above. Check out the video by Nilaus, he is excellent at explaining things.
Small piece of advice from me, never make your blocks smaller than your biggest train.
However the video does require you to realise that the examples of incorrectly signalled intersection which are included to demonstrate how things break when you use incorrect signalling are signalled incorrectly.
OpenTTD is an open-source version of a very old game centered around trains. It pretty much has an identical block management system to what Factorio uses (as well as more advanced options, which Factorio also has equivalents to). It's a bit of a complex game with a daunting learning curve, but...so is Factorio, so that shouldn't be an issue. Certain rules you learn the hard way in 5-10 hours of OpenTTD could save you endless headaches MANY hours later when using big train networks in Factorio.
The basics of naming stations, sending trains to stations, and giving them orders for loading/unloading is all pretty similar in both games. As you scale the rail network up to include many trains running the same route, and intersecting or diverging routes, you will be forced to learn the basics of how blocks work. Then you will learn the hard way, how to avoid getting intersections clogged with multidirectional traffic--or worse, blowing up trains on accident by colliding them head-on! The length of trains will have to be accounted for in block design, junctions will have to be minimized or optimized, etc.
Dosh's video linked above really is excellent, and covers all these aspects, and it only takes you 3 minutes instead of 10 hours. The question is how much of it you can reasonably absorb, and translate to gameplay. For some people, they can only "learn by doing" so to speak.
Maybe I should watched the whole video before making comment :(
I've launched rockets before without ever having to touch trains, granted that's because I cranked the richness up to like 300%, but I've never made a mega base before due to the issue of the post. I feel like once I get the foundation setup for the system I'd be good to go, because then afterwards like you said you can just connect a patch to your system and then your issues are gone. It's just a matter of getting that basic foundation setup with the lack of knowledge that I have.
I think the best thing for me to learn would to just be to start from the ground up. I have knowledge on everything apart from waiting areas and station limits, but that knowledge is more than likely improper and could certainly be improved on. It's easy to run one train on one track, but anything more than that and my brain explodes on trying to figure it out.
That knowledge alone is sufficient to build megabases based entirely on trains, running on one, big rail network. Anything more than this will involve circuit network usage.
Designing in this way, you can get an idea that you could totally reasonably do this kind of train system.
Secondly, even when you need to make 1 single intersection of 2 such bi-directional train paths, you should be able to do it just by putting in some rail signals near the intersections. Observe for a few minutes to work out some kinks (since it's your first intersection like that) and then you'll be good to go again.
Thirdly, if you actually want to do more than single bi-directional paths, and do something like parallel paths travelling in different directions for multiple trains, then there are already blueprints out there for you to use. You don't even need to understand railroad signalling, because the blue prints already put all the signals in for you.
You just lay the blue print how you want it (usually parallel lines, T-intersections, 4-way intersections, turn-arounds or loop-arounds, stackers, etc) and then you put on your trains. The blue print templates are very amazing in this regard that they've already got the signals taken care of for you.
And to grow your trust in those blueprints, don't use them in your ore network yet. Pick a bare spot, build up some those blueprints using some train stops, make your trains automate to many train stops, and watch how your 2 or 5 or 10 trains that you put on this test network, don't crash into each other, because the blueprints and the signalling already work!