Hello @zcampbell ,
Nice to see that you are using our products
I don't think I can recommend to you "the best documentation" for our product. Let me explain a bit about how our toolbox works and why the options are a little bit different from the RM.
The Reference Manual is that document which describes all the capabilities of the controller. It describes the registers and the bits that have to be set in its registers in order to achieve the desired functionality. I think this is the most complete manual. Well, Model Based Design Toolbox does not configure the registers directly. I mean, the MBDT generates C code based on the S32SDK for Power Architecture which is linked here https://www.nxp.com/design/software/development-software/s32-sdk/s32-software-development-kit-for-po...
The SDK makes sure that the registers are set correctly and in the right order. It is a mature product already validated so this is the reason why the settings are not 1:1 with the ones presented in the reference manual.
For our blocks, we have examples and a helpful documentation that describes a bit the settings from the block masks.
Now, if you are interested in a certain topic, as for example the ATC - CTU - PWM synchronization and you want to learn first about this particular case, regardless of MBDT but with focus on hardware capabilities and right techniques, then on the Controller's Documentation page here, https://www.nxp.com/products/processors-and-microcontrollers/power-architecture/mpc5xxx-microcontrol... you will find some application notes. For example, AN12017, 3-Phase PMSM has a chapter describing the CTU triggers, ADC conversion and interrupt timing. Which is the subject you are interested in.
Last but not least, in this community, there are a couple of Motor control Courses, like PMSM Control Workshop and BLDC Control Workshop. Both courses explain motor control theory based on the MBDT toolbox and we believe this is a great starting point.
If you have any particular cases regarding the MBDT examples or functionalities, just ask us on the MBDT Community.
Hope this helps,
Marius