Ok, i try to give some pointers for the signalling system.
Usually i start out with two stations, one connection line and one train, no signals. If you then set a train schedule, everything should work fine.
Now i assume you put another station next to each existing station, meaning you got 4 stations in 2 groups, and one line connecting these stations. Pathfinding for trains only "sees" the rails and signals, not the trains moving or waiting on the tracks. So to prevent them from crashing into each other, you need signals.
Every signal splits your track into blocks, as mentioned earlier. If you hover over a track, it will tell you the block number. Each block can only be occupied with one train. If this is the case, the signal before this block will turn to red.
Now for the signal setup:
First, i try to identify the blocks i want tho have.
Some basic rules:
If you place only one signal next to the track, trains will only enter the block from one direction. If set the signal, arrows will show you this direction, the signal has to be on the right side of the track (direction of desired train travel).
If you place one signal on each side of the track, trains will be able to enter the block from both directions.
On any one-way track, you can place as many signals in sequence to each other as you like. With this, you can create waiting room before stations or connections.
If you want to build a two way track, you have to make sure, that any train in this block is able to leave the block! This means, for two way tracks,
NO signals in this track. Only place them at the beginning and at the end of the two way-segment.
It is really hard to explain all this with words, so here is one picture:
For the picture:
The yellow arrows represent my two way track towards the main base. The blue arrow depicts the track towards station A. The red arrows shows the direction to and from station B. Again, in the north, there is a second two way train.
Example A: Train from Yellow to Blue and back:
The train arrives, continues past the first two connections. At the third, it can only go right, because of the signal placed just after the junction. If the next block (the station) is occupied, it will wait there. For a slightly better setup, the signal should be a little more away from the junction. Until the train is past this signal, the whole two-way train will be occupied, a no other train can enter this block. As soon as the train is past this signal, the track is free, and any other train can use it. On the way back, the train will do one small loop, and arrive at the next signal. In this picture, it is the right one currently showing red, as one train is approaching. If any train is on the track, the signal will be red and the train hast to wait. The important part here is, that any incoming train will not be block by the waiting train. As soon as the track is free, the train will move towards the main base.
Example B: Train from Yellow to Red and back:
The train arrives, and wants to go to the north. This is not possible at the first junction, due to the signal placed here. So it has to take the second junction. The signalling works the same way as with station A, exept, that there is another two way track towards the station. Again, as soon as the train is past the signal, the whole two-way track will be signalled free again. Same thing on the way back. The train arrives, hast to wait at the leftmost signal, and can continue as soon as the two way track is free. This setup can also be improved by adding a second signal to each track in the waiting area in order to "clear" the track and still be able to wait for the next block to be free.
Again, in short, the most important things you can see in my picture:
No signals on the two-way segment.
Waiting areas, so every train on the two-way segment is able to leave it without beeing blocked by waiting trains.
I hope this will help you a little bit and make things more clear.
So, try at first to make a very, very small railway network, first a circle, then add switches and so on. Look at the signals, what will happen with them, when a train goes on it. Think in "blocks", a block has a number, which is displayed, when you hover the rail, every train in that block will set the signal "before" that block it to red.