Hi Herraiz,
I just wanted to chime in. Based on the RomBOOT message you get, I think the section “Installing Atmel SAM-BA Utility” is the one to follow. I don’t believe you need to make any hardware modifications. The SAM-BA utility monitors for special characters on the debug port. If you were NOT getting the RomBOOT message, then the bootstrap would be okay but U-boot would be failing and that is probably where the hardware modification is necessary. The RomBOOT message is coming directly from the Ateml processor’s ROM.
Regarding where the files are located, I’ll let Bryan help you with that.
Best Regards,
Darrik