Relationship between TeensyTimerTool and Pins

I am having trouble using TeensyTimerTool timers correctly.
I am using T3.6s .
My experience level is greater than Arduino Uno but well below the level of many contributors on this forum.
My question is: "Is there a relationship between timers and pins? Does my use of timers affect what I can do with particular pins?"
My project uses nearly all the pins on my T3.6s.
Yes, if you need PWM (analogWrite), you need to make sure not to use one of the timers which generate the PWM signal for this pin. Here some information and a list of which timer generates the PWM for which pin.

I'm not aware of any other teensyduino core code the TimerTool might clash with. Of course there might be libraries using some timers under the hood which might clash with the TimerTool but that can't be prevented I'm afraid
At least I'm not aware of any issues. Have a close look at the other libraries (if any) you are using. Or better, just try...

Edit: just saw in #1 that you have troubles. Can you describe what doesn't work? Some code?
I need to do a lot more work to pin down the problem area and separate it from other possible issues. The difficulty is most likely ignorance on my part. The initial problem appeared to be an unexpected interaction between DMA-generated interrupts and timer interrupts. I can't supply code until I've done a lot of cleaning up(!). Thank you for your advice, I'll come back in a week or two when I have a clearer picture.