You can hit the upper engines from the lower engine area, but the total repair time for all engines isn't all that improved. You have the option to hit:
-Hit a side engine, hit the middle engines, run to the final engine (slowest, safest)
-Hit a side engine, run to the middle engines, jump to the last engine (fast, unsafe)
-HIt a side engine, jump and smack a middle engine, run to the other side engine and hit it, jump and smack the last middle engine (moderate, safe)
Overall this is one of the slowest engineer routes for engines, you can even get the mobula engines faster (the slowest is probably a junker, but you can divide your forces better on a junker). Which is kind of hard on a ship that really relies on it's engines and pilot tools so much. One of the reasons the pyra is so powerful is because it's components are incredibly close together, allowing intense amount of abuse to the components.