Our programming team is doing the same thing. Here is the advice I gave them.
There are two parts to this.
PART #1. Programming the LED lights to do what you want. Like light "behaviors" let's call them.
PART #2. Interfacing the CRIO to "trigger" the arduino to run a behavior.
Part #1 should consist of you writing code in the arduino to make your LED lights do what you want them do to.
For example write down the behaviors.
1. Robot is idle
2. Robot is shooting
3. Robot has the ball
Now write the code to make the LED lights do what you want for each behavior, then place them into a while loop with a CASE SELECT structure.
CASE 0
Robot is idle
CASE 1
Robot is shooting
CASE 2
Robot has the ball
etc...
Part #2 is setting up, wiring and programming an interface in the CRIO...
There are three INTERFACING suggestions I can suggest.
SIMPLE INTERFACE
Wiring the output pin of the CRIO to the INPUT pin on the arduino.
Map the CASE SELECTs to a digital input on the arduino.
Then in the LABVIEW program, just turn on a digital output that is wired directly to the arduino.
IN1 = trigger idle state
IN2 = trigger robot shooting
IN3 = trigger robot has the ball
This interfacing method is called discret wiring I/O. It's the simplest interface of the THREE interface suggestions I have for you below.
INTERMEDIATE INTERFACE
A stepup from that would be to do a BCD (binary coded decimal) ENCODE from the CRIO to a DECODE in the arduino. The advantage is you can have 8 robot behaviors with only three wires connected. It's technically the same as discret, however you're not chewing up a bunch of wires to get more behaviors.
Wiring I/O on the Digital Sidecar sample.
(least signaficate bit on right)
BINARY VALUE 4, 2, 1, etc...
IN3, IN2, IN1
0,0,0 = 0 decimal
0,0,1 = 1 decimal
0,1,0 = 2 decimal
0,1,1 = 3 decimal
1,0,0 = 4 decimal
1,0,1 = 5 decimal
1,1,0 = 6 decimal
1,1,1 = 7 decimal
ADVANCED INTERFACE
One more suggestion would be to write an I2C interface.
In this case, you will need to include the wire library and setup a SLAVE ADDRESS to the arduino and have the CRIO become the MASTER and set memory bits.
http://arduino.cc/en/reference/wire
So first you have to decide how you want to interface the two processors together. That's the root decision you need to make first.