If your problem is that a train is going from the main line to the branch line and crossing the opposite line by means of a diamond crossing then, yes the AI does not regard this as an obstuction and will signal a train on the opposite line normally and if it is timed right the train will pass straight through it without crashing. The link as posted by Lynxfan will give you an alternative method of signalling. I hav,nt tried it myself as it appeared a bit complicated. There are other methods however. My favourite is to remodel the junction. Instead of a diamond crossing you have a main to main crossover followed by a single point switch to take you onto the branch. If the branch is a single line this method is a more realistic way of doing it. If the branchline is double track then you would also have a 2nd point switch which brings you off the branch onto the mainline. You could also try a simple trigger rule but this is more restictive from an operational point of view and may only be useful for a specific scenario. You were also unsure about signals and what a particular message meant. Difficult to explain without seeing your route but in your case if you have a double track mainline and a double track branchline you need 6 signals for the junction. One on each track approaching the junction, each of which has a another signal in rear which acts as a distant. Don,t forget to add yellow direction markers as needed. The signal taking you from the main to the branch should have a feather route indicator and not a theatre type. I could add a lot more but this post is awfully long as it is. Feel free to post further questions, the more specific the better.
