The YIN is used to force a signal to yellow instead of green and is generally used to indicate a speed restriction. Normally the lights will alternate between green and red depending on which route the switch is set for.
For example, if the switch is set to enter a siding using the YIN would give you a yellow for that route instead of a green indicating it's okay to proceed but at a lower speed
I have never used the RIN
Also, in addition to the control boards that come with each signal, did you get any TSC's (Turnout Signal Control). This is the board that sits between the tortoise machine and signal control boards.