AVR Studio cannot access to bootloader on your Axon. You will either need to follow the bootloader instructions to program by USB, or purchase an ISP programmer to program by AVR Studio.
For modifying a servo, your microcontroller just needs to send a 'zero' command. Your software will say 'go to position zero' by pulsing the servo signal line (any I/O pin on the Axon is fine). Then you rotate the pot until the servo stops rotating, and glue it into place so it doesn't shift with vibration.
If you are still confused, just let us know.