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
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.