Fuel is barely noticeable as a problem. In fact, I've never even considered it so far. Enemies provide so much of it for basically free, even when you've maxed travel distance. At least until you start hitting very high sectors where there are essentially no enemies (a different problem of its own).
prestige resets the tree, though im not sure it gives anything at all. if you dont press your skilltree before clearing sector one, you ll have enough experience to preserve first 5-6 modules. usually only homing/pierce/and maybe shield restore or a module with 3 chips like proc/shield restore/mulishot something if placed high enough are critical. besides it looks like your weapon upgrades ones you bought in maintenance depots or how they called stay intact on prestige, so you pretty much only need homing/pierce to blast. well and not get into lv 11-19 elites maybe