this can be a bit complicated:
# You have to add the debugger to the settings:
1) Settings->Debugger->GDB/CDB->Create Config-> Enter a usefull name like ARMGDB
2) Switch to the new configuration
3) Executable path-> Set the path to the the gdb in your arm toolchain folder
4) Untick "Enable watch scripts", "Disable startup scripts"
5) Ok
# Set up the project
1) Project->Properties->Debugger->Select target:<Project> ->Remote connection:
Ip address: 127.0.0.1 Port: 2331
2) Additional GDB commands:
3) Ok
Now you have to start the gdb server for the ATMEL-ICE. Then you can run the debugger...