As long as the coals burn out (bad smoke) before the fruit wood the wood flavor will cancel out the charcoal. Same goes for if you have to add charcoal during the cook. Overlay with wood that will burn longer than the black and no problems.

That's why in a long cook you want chunks of fruit wood, dunked in water the night before, so they last. Wood chips only work in a direct cook scenario like steaks.

Also, think light on the wood. You want just an overlay of smoke taste. Keep in mind that the smoke flavor gets more intense over time so something with a little smoke flavor will be a LOT the next day and onward. Don't go by the smoke you smell during the cook!