The unit you give the order to will burn the structure after 15 days, basically a full turn plus one day. You can give the unit orders to move with a destroy fort order active, they will complete the arson and then begin to move.
The destruction is guaranteed as long as the unit stays in the region for the 15 day duration.
The most efficient way to implement destruction? Ask Oppenheimer.. He did a good job in New Mexico..
But ya, there are a lot of stockades out there. I'd go for the ones with the largest stockpiles first. Maybe try to concentrate on creating large dead zones. Mounted partisans might work well to harass forts that do fall to the enemy; they have a pillager trait that lets them instantly burn depots and stockades on capture. There may be some generals who have the pillager trait as well, maybe Quantrill.