I believe that PID algorithm doesn't need knowledge of time since start. Oftenwise, PID code is time-invariant, and might not need timescale at all. For example, timing comes from ADC sampling which runs on its own clock.
I recommend to post your project here for review. File->Create Workspace bundle->minimal.
I'm with BoTa, there shouldn't be any need to know the time since start. However, if you still need to have this information, you can hook up to the SysTick timer, which is configured to 1ms by default.
The boot component provides the mechanics to do this. You can hook up up to five callbacks. So, you can write a callback and increment a variable each time it is called. Keep in mind that the variable must be defined volatile. I don't know how it's implemented in Arduino, but going the mentioned way would mean that the mechanism begins to work after the call to the callback configuration. So it's still not the time from (power) on or reset.
You can find the information about the relevant functions in system reference guide for your device.