As with city driving, it's better to know the general location of where you're going instead of relying 100% on Waze or any GPS app for that matter.
For example, you're going to Baguio. Very simple - NLEX, SCTEX, McArthur Highway, Kennon Road, and then voila, Baguio. If Waze suddenly brings you to an unknown road, don't follow it.
I drive thousands of kilometers of provincial roads in a month, and have found myself needing Waze a few times. 90% of the time, Waze gets it right. Though when in the province, I alternate between Waze and Google Maps to be sure. For the 10% of the time that Waze gets it wrong, I just trust on common sense, and if necessary, I ask locals.
People were able to drive from Luzon to Mindanao long before Waze existed, I don't see why the app should be a limiting factor today.