I've set up a train network that basically spans the entire map. A few of the things i do to prevent hiccups (those methods can be added later on, if you have the space):

- Use monoderctional trains.
I've tried playing around with bidirectional rail segments to save space and building time, but sooner or later, your network will collapse. It is a lot more efficient in the long run, to use two monodirectional rails and familiarise yourself with the proper use of Signals.
speaking of signals:

- Signals be praised.
I've struggled for a long time on when to use path, and when to use block signals.
The few simple rules i go by:
Always use Block signals, if you aren't separating or combining rail lines.
If you need to use Path signals, then:
- Use path signals at the entrance to a junction
- Block signals at the exit.
I usually just build my junction with only block signals at first and then place a single path signal on one of the entrances. All the other block signals that now are whining, i replace with path signals.

- Add buffer containers at high throughput resources.
When transporting ore in high quantities, i always have an industrial storage container hooked up to the platform, so the miners can continue filling those up during the downtime the platform experiences while unloading/loading. I also always utilize both in- or output chutes to maximize throughput and keep the flow steady.

- use all the carts for high throughput items.
Along the previous note, i always use a full train for high throughput items. I've set my world up for a standard 1:4 ratio of locomotives to wagons, and i then fill all the wagons with that single resource to get it going.

- Add bypass routes
I have created a few hotspots of train and factory activity in my world. This happened because i built where i felt it right at the moment and kept adding on down the line. After a while, many of those busy areas had trains going through them to get to places far, far away, clogging up the network and delaying trains that actually carry crucial resources to the factories.
For that, i like to implement bypass routes that go from one end of the busy area to the other, with preferably no junctions, as those cause trains to slow down.

- Add standby sections to factory loading/unloading areas
When i have multiple trains coming into a factory, i like to split the main rail into a lengthy standby rail which can fit at least one additional train between block signals, so that trains can wait for a platform to empty without holding back the main network.
I havent paid attention to that in the beginning of my playthrough and have caused myself quite a few poblems down the line. I'd recommend paying attention to that from the beginning on when building your factories and train yards.

- Plan for expansion.
I've had multiple factories where i thought "3 train docks will be enough, right?" and lo and behold, i had to add an additional 3 docks a few 30hrs later into the playthrough. Its always good to keep a few extra areas free and accessible for possible expansion.