the atmel avr is connected via the UART interface to the BeagleBoard. in order to properly communicate with the atmel, you will need to make sure that either your bootloader or kernel properly configures the two pins used for UART2 TX and RX.
if you are using one of the many angstrom builds for the BeagleBoard, the Trainer is automatically detected via the i2c eeprom, and the pin muxing for UART2 is done.
Dave