Thanks, I was noticing that myself. I've spent the afternoon studying the data sheet. Holy cow it is VERY large and there are MANY MANY features of this thing. Some of which the Due doesn't even expose. For example, there are two hardware quadrature encoders. I just spent the last 2 weeks ironing out extremely efficient interrupt routines to do the same thing. I learned the pins those lines are connected are available on my project if I re-route pin 2 so I can use Pins 2, 13, an A7 (AD7) not sure which yet for the index pulses. I may do that when I get to it but for now the interrupts I've written seem to be doing a fine enough job.
I did find the 4 bits in the register that are used for managing the CS pins. Did you know you can configure them to be addresses that feed a built-in MUX allowing you to manage up to 15 or 16 total SPI devices all on the same TX/RX pins? Crazy, crazy.
I also re-read the datasheet on my chip and it technically isn't SPI. it's really 3-wire or something like that. It has SCLK, DataIn (MOSI on SPI,) and CS. Then there is an error pin which could technically be the MISO but wasn't designed as such. Still it's desirable to use it so I'm not burning other pins I need for other things so, yes I've resigned myself to using a separate I/O pin for CS.
Given all the above, I'd like to find a way to use the CS lead that actually isn't connected to any of the Arduino pins because right now I'm burning a digital pin I actually kind of need (52) just because that's the default in the SPI library and IS NOT the one that actually controls chip select.
Also, I discovered that Timer 1 channel 0 must be used with SPI somehow because when I use that timer to manage another function it completely disables SPI. I've moved my timer interrupt over to Timer 1 channel 1 and now both seem to be working again.
I'm wondering how that will affect trying to use the hardware quadrature decoder with SPI as well. So many possibilities, so little time....