See the block diagram for high level function and connectivity. The timer interacts with the CPU core and the power manager and reset manager to drive wakeup / reset events and interrupts. There is also an extra input to tell the counter whether to run ("counter-run"). This is used to stop the watchdog timer running when in debugging mode or when the alert handler has put the system in a "killed" state.
The always-on timer will run on a ~200KHz clock. The wakeup timer is 64b wide and the watchdog timer 32b wide. This gives a maximum timeout window of roughly ~6 hours for the watchdog and almost 3 million years for the wakeup timer. For the wakeup timer, the pre-scaler can be used to slow the count down so the counter value matches some desired time unit (e.g. milliseconds).
Register reads via the TLUL interface are synchronized to the slow clock using the "async" register generation feature. This means that writes can complete before the data has reached its underlying register in the slow clock domain. If software needs to guarantee completion of a register write, it can read back the register value (which will guarantee the completion of all previous writes to the peripheral).
The wakeup count and threshold are both 64-bit values accessed through two 32-bit registers. It is not possible to do a single atomic read or write of the 64-bit values. The programmer's guide suggests some ways to access the wakeup count and threshold to avoid issues from race conditions caused by this.