Sending command through USART.

I am new to this kind of communication. I am able to send command from PC to AT90USB1287 microcontroller as well as able to get response using USB communication. Now i have connected another microcontroller(ATmega32) to this board via USART communication. I am trying to send command from PC to this board. Both controllers have different commands. So i have created an array containing both controllers commands in AT90USB1287 controller. My concept is compare the incoming command from PC with all commands in array based on result i am trying to send commands to ATmega32 controller using USART.
Can anyone help me how to fix this? Do I need any conversion here? If so, please help me with an example.