The trains aren't that mad to figure out.

• Chain signals into crossings/junctions, block signals out.
• This also applies to any track section where a train can block other trains.
• Signals and stations only work to the right of the travel direction
• Signals without another signal on the other side are strictly one-directional.
• you can mismatch signals of any pair, i.e. a block sig opposite of a chain sig.
• Using signals within a junction can be useful to improve capacity of said junction, though you must use chain signals for that.
• Always make sure your longest regular train can fully leave a junction/crossing/flow-critical block before it hits another signal.
• Having one train length across your entire fleet can make this easier to wrap your head around

As for station stopping instructions, that'll take a few more lines to go into.