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The main configuration options for Watchdog are the polling interval and the CPU usage threshold. 

Polling interval

The polling interval specifies how often Watchdog will gather statistics. The more often this occurs, the more likely a misbehaving process will be flagged. However, this will consume more processing time which will reduce battery life

CPU usage threshold

This is the CPU percentage that will trigger alerts. This is measured in CPU usage over the polling interval

Real time polling interval

If you check the real time checkbox on the CPU tab, this is the interval that is used.

Include phone processes

This will poll all the processes on the phone, not just the Android ones. This will take a bit more processing time for Watchdog, but will give you a more complete view of the phone's CPU usage.

Display all phone processes

This is an option on the prior config. If not selected, all the non-Android apps will be rolled up into one entry on the CPU tab. If you want to see a breakout of that it consists of, select this option to see all the phone process data.