I want to use an external clock signal as an interrupt for the Due timer. How do I do that? I could not find any info on this on the net.
Everything you need to know is in the SAM3X datasheet:
However, as Atmel's datasheets are some of the most cryptic ones around, you'll need to spend quite some time deciphering it.
There's an entire section just on the timers. It tells you all about how they work, however, relating that to which registers you need to set to get it to do that is not clear (as is normal for Atmel) since the registers are listed elsewhere in that section with no real relationship between them.