with capture inputs.
Have you checked that the capture inputs are broken out? It looks to me that the following TC IO pins are available
TIOA0
TIOB0
TIOA6
TIOB6
TIOA7
TIOB7
TIOA8
TIOB8
So that's 4 TCs with 8 potential capture inputs as I understand the hardware. But if you are generating waveforms as well you may lose some of them depending on how you are doing it. TCs are pretty complicated, I haven't really got my head around them yet.
Can just about manage with only 3 timers but would have been stuck if millis() had pinched one!
The SAM has 9 32-bit TCs in total, you could normally afford to lose 1 or 2 for the system, but as I said I don't think you will.
Rob