I was just thinking of a line in Apollo 13, where one of the characters are explaining something about halfway there and moon does the rest of the job for you so I was just thinking if their were engine troubles that would help the ship get back.
That's not how it works. The entire orbital trajectory is shaped by the interaction of the gravitational fields of both the Earth and the Moon. Orbit, by definition, is an unpowered trajectory shaped by the effect of gravity on a free-falling body. The Apollo spacecraft fired their engines only a few times in the course of their journeys, "burns" that changed their trajectory to put them into orbit or take them out of orbit, plus occasional short burns for midcourse correction en route. Mostly they let gravity do the work. Here's a diagram of Apollo 13's voyage with the engine burns (corrections to finesse their course and injections to change from one orbital path to another) called out.
A leader surley must have a degree of knowledge, what does Sara know about commanding a ship from the future and temporal mechanics.
No. A leader gets knowledge from her advisors, like Kirk gets information from Spock, or like Jack O'Neill gets information from Daniel Jackson and Sam Carter. Or, for that matter, like Oliver Queen gets information from Felicity and Curtis, and Barry Allen gets information from the STAR Labs brain trust. The leader is not necessarily the smartest person in the room. What a leader needs to know is how to lead people, how to get them to unite behind a common goal, how to win their trust and loyalty, how to bring out the best in them. Rip failed at that, and Sara succeeded.
The writers have always rushed this aspect of the show, the technology must be so COMPLEX and somehow Jax became chief engineer with zero training because he works on cars back on Earth and Sara now commands the ship.
"Zero training?" Have you been paying attention at all? It was established at the start of the season that Rip had been training Jax for months during the break between seasons, teaching him how to repair and rebuild every system aboard the ship, because Rip anticipated that he might not be around forever and that someone would need to take over just in case.