Help with LogomaticV2 Project

Hi i am building a measurment system based on SparkFun logomatic V2 board

https://www.sparkfun.com/products/12772

I want the system to be controlled from a screen ,for that i have an arduino mega thats connected to the display

what i need now is to connect the two boards togther i want :

  1. to be able to start and stop a measurment from the arduino

  2. to be able to acces the sd card on the logomatic from the arduino and see what files are there

  3. to be able to costumize the configuration file on the sd card on the logomatic

on the board i see that there are pin holes labled stop,reset,usb and also pins for SPI comunication

but i can not find any documintaion thats explained the functionality of those I\Os

on the simplest level of course i can turn the power of the logomatic on and off and by that i make new fies , but i want more control than that.