put a cobblestone structure pipe next to it with a simple gate, it might be one of the options in the gate's interface. Have it emit a redstone signal when it has work, and feed that to the engines to turn them on/off.
alternatively, or if it doesn't have the condition, the same pipe gate on the chest you're feeding into and use a "has items in inventory" condition to turn on the engines, then you just need to prime the quarries with some power and their internal buffers should be enough to get through any small to moderate sized voids in the quarry. This of course takes into consideration you're auto sorting from that chest (IE enderchest etc)
but if you just used energy conduits, they won't explode, but the engines woudl burn through all their fuel once the quarry was done.