The engines can be in push-pull configuration, or stacked on top of each other, to keep them on the centerline. If that can't be done then simply put them as close to the centerline as possible. Put more (presumably smaller) engines on the aircraft so that the loss of a single engine has lesser effect on performance. A larger rudder further back would help also.
I recall reading about someone that built a custom light airplane to fly over the Amazon forest. As I recall it was to take close up photographs of the canopy. A concern was an engine loss over such a remote area, and in the low altitudes they'd be flying. The plane had two pusher props close to the centerline and a larger than typical rudder. This was so it could fly for extended periods on a single engine and not fatigue the pilot. I also recall that they'd kill one engine in flight so they could fly slower and get better pictures, which in my mind negated much of the advantage of two engines.