A ship that size will require solid 10x10x10 blocks of reactors. Spacing them out does not matter because once he reaches around 1,000,000e/sec in generators, the game caps any further increase in generation.
For thrusters I find they generate more thrust if they are all connected but that is just me. Ships I make are too big to mess about with intricate designs (and I also found that a lot of people who do, waste a LOT of space which by extension increases the size of their ship and lowers it\'s maneuverability).
It\'s up to OP to really decide what he wants to do with it.
Forgive me for intruding but I also don\'t think that AMC\'s on a ship this size are a good idea. From experience, they don\'t perform as well as they should. A ship 1000m in length will have THE slowest possible turning speed, severly limiting what you can actually attack whilst piloting. Capital ships, maybe. Planets, maybe. But anything smaller than a Cruiser and you will struggle to keep up with it. Not to mention, the enemy vessel can simply fly around you. Even when fighting a matching opponent, it will be tricky to keep him in sights (and range) to hurt him if were to fly into you and slide above the reach of your cannons.
I much prefer outsourcing the armanent on ships this size to turrets exclusively. You can set the biggest ones to attack selected targets which will give you the freedom to track your opponents wherever they go. Then have smaller turrets as proximity defence and auto-attack for closer ranges. This way, you just fly in and watch as enemy fleets crumble. That\'s just my opinion though.
TL:DR: Don\'t sweat about reactors, just do 10x10x10 blocks and cram them in everywhere you can cuz it doesn\'t matter past 1,000,000. Do the same for shields, EVERYWHERE. Use them as filler.
For hull inspiration, you can always research sci-fi movie and TV ships, or take some ideas from EVE online. Be creative, think of something unconventional.
