@Patouf
Don't know if it will help, but there are RTC register definitions buried deep in the folder tree at e.g.:
... \arduino-1.5.1r2\hardware\arduino\sam\system\CMSIS\Device\ATMEL\sam3xa\include\component
Look for files component_rtc.h and instance_rtc.h (there are multiple versions in the tree under the ATMEL folder).
HTH
Jim