There is a bug with old Arduino bootloaders, you have the following options:
#define BOOTLOADER_BUGFIX "234fs34567hf"line in your
APM_Config.h, replace the string
"234fs34567hf"with some random characters and try to upload the firmware again.
If you can move your sticks and the flight controller seams to not register any of your inputs its most likely you forgot configuring your correct RC Input type. Please refer the General Configuration documentation.