My first advice, YOU NEED SUPPORT SHIPS! Tankers and cargo ships! You said you don't have enough ships to carry fuel and stuff, just place cargo and fuel ships in your fleet! in the start I had 3-5 colossus on my fleet to carry loot to sell, and 2-3 fuel carrying ships, also 2 salvage rigs! You will need a starliner to carry crew to colonize planets. You should have around 25 ships with you all the time, 15 combat, 10 non combat and with space to look new ones. Story unused ships in abandoned stations for free and get them when you need it! Insulted engines and improved manutention in the big ones, always check what are giving away your signature, normally big civilian ships need insulated engines, but if you have capitals, small civilian ships don't need to insulate. Get insulated capital cargos and tankers when you are rich.
NEVER, EVER militarize civilian ships, they will lose all the bonuses they get from the industry skill, just insulate engines.
My colony guide:
SINGLE SYSTEM, SINGLE SYSTEM ONLY!
Have 20 million in the bank, not hard if you have a commission and is doing contact quests and bounty hunting, selling 6k fuel to the pirates on Umbra each week buying it from the Sindact capital on the SAME SYSTEM, will give you 300.000 each week.
Scout all places, try to find a system with:
In order of importance:
One or two habitable planets with a farmland, it can have a -1 farm, if it has no transplutronics resource. because soil nanites will compensate for that, you can even colonize a -1 farm, because you only need food = pop to sustain your colonies the +1 from the administrator or your skill will compensate the -1.
One planet with no atmosphere. For refining and fuel production.
One planet with +0 organics, so you can sustain your light industries and planets with that are not habitable (they demand organics and food to live there).
One gas giant with plentiful volates +2 production, need to be a gas giant because of the item to improve production, it can't be a +2 volates ice world, because it you can't use the improved item.
You can go with a +2 volates (no gas giant) if you don't plan to use the item to compensate cold and poor light worlds, or 0 volates gas giant. But they are normally cold planets so, what the point?
Habitability WILL hurt a lot during the early phases, because the 50.000 hazard pay to make the colony grow, but they are not really and issue in the end, my planets are 125, 150, 200, 225 (down from 300) and 250, all give a 100.000 profit, just the 250 one won't, just 30.000 but I wanted to have 2 very hot planets to have a really big defense force.
First I had to clean the system from the REDACTED, just wait when they leave the nexus unguarded and kill it, don't do it in all system, because you need some systems with nexus for REDACTED farming for alpha cores, that was a mistake I did on my first game.
My colonization plan:
First world, water 150%
-1 trans (so no soil nanite to improve farming), 0 ore, 0 food (normal on water world). +2 organics (my only organic source), but it have a solar shade that increase farming +2.
Colonized with 2000 food, 2000 supplies, 2000 fuel, hazard pay, to sustain the colony for 15 days before the starport goes online. This stockpile is optional, it is better just don't pay the hazard pay and wait that 15 days, before start paying it, because your colony can't decrease of size, I do it for roleplay proposes.
Queue the farm, ground batteries (+1 stability), patrol station (+1 sta), starbase (+1 sta), waystation (+20 accesibillity), and upgrade the starport to megaport as soon as the starport gets completed, accesibillity and stability gives you a lots of grown bonuses and extra money, so, build all infrastructure buildings in all planets, just not the planetary shield.
On the same time I colonized the no atmosphere, very hot planet (200 hab). Did it too early, should have waited the water planet to get lvl 4 so I could mine the organics that the planet need for upkeep, so it costs lots of money, plus the +50k hazard upkeep on it. Started refining on it, to pay part of its upkeep importing the ores, next was the fuel production, both need a no atmosphere planet, but I wasn't using the items until they all got size 5.
As soon as the water planet reached size 4 and started mining organics, colonized the arid world (125 hab), and build a light industry, wait for the stability buildinds to get online and freeport on it! Freeport are great, but remember to build your defenses, people will attack it, but because you have 3 patrol hq and a station on that planet, the first attacks will be easy to defend. This will be your first planet to reach size 6 (maximum size) and your first profitable one, because of drugs.
I didn't want to to deal with panthers, so all my items to improve the mining, refining, fuel, orbital lamp and the light industry were not in use until they were all size 5.
Colonized the gas giant with +2 volates, (300 hab) and now I really started losing money, but in the end it is my most profitable colony, because the orbital lamp decrease the habitability to 225, that is acceptable. Too bad I installed it when it was size 4 and couldn't pay for itself. Took me a while to install a gamma core in the pop infra so it could pay itself.
Also colonized a very hot light atmosphere for defense propuses (very hot planets are where your big defense fleets come from).
In the end
All planets have all infra builds, and the freeports one got shields.
All planets I use 2 story point to improve the mega ports.
All planets have tier 3 low tech space station. (personal preference, hate the midline (it was greatlly improved in the patch, but still hate it) and think the soft flux of the high tech one is bad)
Water 150 Freeport
Megaport (item to improve acess)
Farm - mining - light industry (item to improve) - HQ
106.000 profit
No atmosphere very hot 200
Refining (item to imp), Fuel (item to improve), HQ (Item to improve) - commerce.
120.000 profit
Desert (125) Freeport
Light industry (item to improve) - Farm (item to improve, so the -1 is a +2 like the water world with the solar shade), refining (because it had a free slot), and HQ
110.000 profit
Gas giant (225, down from 300)
Pop (orbital lamp) gamma core
Mining (improved item volates), commerce (item to improve), Heavy (syncron core), HQ
99.000 profit
Left over very hot planet 225 (colonized it because you can have 5 planets without using AI, 2 for you + 3 admins)
Pop (gamma core)
Mining (item to improve, so -1/0 goes +2/+3), Commerce (it almost don't pay for itself, trying to find the improvement), Heavy industry (sync core), HQ (Improved)
20.000 profit. Almost don't pays the administrator on it, but existis to defend the other planets.
With 3 HQs and 2 very hot Improved HQs I fear no one, and paying the upkeep of my admins, 4000 crew and 1500 mariners, I still profit 300k a month.
Control around 33% of all markets only improved all megaports with 2 story points each.
I do have a hypershunt close and 3 itens to use it, but I don't use them, because I would need to spend 4 story points to improve the no atm refining, an alpha core in the refining and a gamma core in all pop infrastructure using them, and any trade disruption in the colony, something that happens a lot, would hinder all other industries on the planet, but I really don't think it is worth it.
Having lots of colonies in the same system, improve access that you lose to be far from the core, all my colonies have around 150% access, freeports one have more, hight gravity have less, and if I remove the waystatons (tested that), the decreased access makes me lose more them double the costs of the waystation upkeep.
Also the system had no stable points, just create 2 with alpha cores and fuel. Build the +1 stabilty and the +2 mov.