Few keynotes:
First and most important everything is optimized to minimize micromanagement.
Minerals should flow in both directions to support large scale industrial activity everywhere and to allow all colonies to build themselfes.
This is not optimal approach in terms of fuel and minerals consumption to operate this logistics chain.
1.13 still and very late game.
You don't afraid raiders and able to reliable counter them.
My empire is always virtually divided in sectors, usually they are 2 jumps from center, but it isn't strict rule.
Center of a sector is usually a center of industrial and shipbuilding activity, but it isn't strict rule too.
Logistics chain is divided in "Sector minerals logistics" where all minerals mined in sector are transported in/out central colony and "Global minerals logistics" where minerals from central colonies of sectors are transported in/out Earth.
For minerals transportation i use separate type of freighters - fast, and <100.000 tonns.
I don't use and research sub40% low power engines, to prevent civilians to use them.
Akmolinsk-F G10 class Freighter 99 997 tons 622 Crew 8 780.9 BP TCS 2 000 TH 32 000 EM 0
16000 km/s Armour 1-191 Shields 0-0 HTK 113 Sensors 0/0/0/0 DCR 48 PPV 0
MSP 2 039 Max Repair 2000 MSP
Cargo 45 000 Cryogenic Berths 600 Cargo Shuttle Multiplier 10
Lieutenant Commander Control Rating 1 BRG
Intended Deployment Time: 4.5 months
Commercial Plasma Core AM Drive 50% EP8000.00 (4) Power 32000 Fuel Use 0.35% Signature 8000 Explosion 5%
Fuel Capacity 700 000 Litres Range 356.4 billion km (257 days at full power)
This design is classed as a Commercial Vessel for maintenance purposes
Sector minerals logistics
Set reserve level of minerals on colonies, usually i follow this guideline:
<500 mln population body - 10.000 of each mineral
<1 bln population body - 25.000 of each mineral
<3-4 bln population body - 50.000 of each mineral
5-10 bln population body - 100.000 of each mineral
10> bln population body - 250.000 of each mineral
Sector central Colony - 500.000 of each mineral
Starting point of transport - central colony.
Central Colony: load Durantium x1250
Central Colony: load Neutronium x1250
and all other minerals types x1250
Central Colony: Refuel&Resupply
Colony: Unload all minerals
Colony: Load all Minerals
Central Colony: Unload all Minerals
and Cycle Moves
If minerals are below colony reserve level - transport unloads all minerals picks up nothing (transport pick up nothing generates event and stop increment, but after colony reserve will be filled everything will go smooth), if minerals are above reserve level - transport picks it up and unloads at Central Colony.
In some cases - large distances or colony consumes minerals very actively or produces them too fast it is worth to add second transport as separate fleet and launch it with same orders as 1st, but with 5+days time difference.
And don't forget to save orders as a template.
Global minerals logistics
Earth serves here as a central minerals storage and point of distribution.
Here everything is bit more complicated.
Summary 22 transports required for each Sector central Colony. 1 for each mineral type from Earth to Sector central Colony, 1 for each mineral type from Sector central Colony to Earth.
From Earth to Sector central Colony, Starting point Earth, hauling Durantium:
Load Mineral Type - x12.500 Durantium (50% of cargo, this needed because if Sector central Colony is above reserve level, it should be able to transport 12.500 Durantium transported from Earth and surplus mined in sector back)
Refuel&Resupply
Move to Sector central Colony
Unload all minerals
and cycle moves
From Sector central Colony to Earth, hauling Durantium:
if colony reserve level set to 500.000 then
Sector central Colony:Load Mineral Type - Durantium and set "Minimum Available" to 1.000.000
Sector central Colony:Refuel&Resupply
Earth: Unload all minerals
and cycle moves
When minerals are below 1.000.000, Earth will supply Sector central Colony with minerals. When minerals are above 1.000.000 Sector central Colony will strart move surplus to Earth.
And keep in mind that Sector central Colony is local hub for Sector Minerals Distribution, thats why mineral reserve level on Sector central Colony and "Minimum Available" when hauling minerals to Earth are different numbers.
So far helps me running this with very rare mineral-related micromanagement: