Handshaking between Arduino and Raspberry Pi

I'm using a Cubieboard, which is similar to Raspberry Pi so I put the Pi in the title for simplicity.

I am trying to do handshaking between the two boards and I saw this post about how to connect the inputs.

However I want two connections. One is output from Arduino to the other board, and the other is input from the other board to the Arduino. What is the proper circuitry for this. Or is there a simpler way?

What I'm trying to do is call a function from the Cubieboard that sends high to the Arduino. Then the Arduino code runs and sends a high to the board to let the other board know that the Arduino is finished. Of course the Arduino is in an infinite loop, so when the function is called again, Arduino seemingly only runs once.

The Arduino will be able to read the 3v signal from the Pi. It is only when the Arduino is sending 5v to the 3v Pi that you need to modify the signal.

...R
Serial Input Basics

What I'm trying to do is call a function from the Cubieboard that sends high to the Arduino. Then the Arduino code runs and sends a high to the board to let the other board know that the Arduino is finished

Are these just logic levels?

If so use the attached circuit:-