-Troops can only be moved via troopships. Remember, it's not just the soldiers, but their huge powered armour suits, all their other equipment, supporting forces, etc. It's the difference between sending a bus and a tank into battle.
-Scientists (and all the other officers and special character) appear based on how many Academies you have. The more Academies, the faster you graduate more experts.
-Civilian shipping lanes will automatically move trade between planets. This seems to give you money. You can contract them to move goods between planets if you don't want to or cannot do it with your navy. For example, set a contract to supply 1000 Infrastructure at Earth, Demand 1000 Infrastructure at Mars, and they will slowly move them for you.
-Maintenance facilities are required for repairing and servicing ships. Each one increases the maximum ship size that the planet is capable of servicing. Maintenance supplies are like missiles, you must actually build them and get them sent out with ships. You already start with a ton, and each ship usually takes only a small amount. However, you might need to make more if you build lots of larger ships, or take extra for a long campaign.
-Repairing in space requires maintenance parts. Adding more engineering reduces the chance of passive wear-and-tear failure, and adds a bit of maintenance capacity for the occasion that something does break. In combat, parts are heavily damaged and require lots of parts to fix, which is what the larger maintenance storage is for.
If a ship has no maintenance capacity, then it basically has no means to repair itself. This could be from simply being designs to be disposable, or from all those components being destroyed in battle. So, you can either try and get a tow-boat, or abandon the ship.
If it simply has no spare parts available, but has capacity, then another ship can fly up to it and give it parts from its own store.