Gates are the proper solution. But then you need walls all along the rail, or need to remember to only cross the rail at these crossings. If you need something quick and dirty:

Connect a signal to a colored light, space them so that you always have at least one of these lights on screen. Or connect the signal to a programmable speaker, and make it play some sound which warns you.

One way to do it would be to connect a gate to your train signals. When the player opens the gate, it should turn the signals red, stopping any train.