Not sure if anyone has already suggested this, could we have a reserve level at colonies for fuel and MSP? this would allow automating to reserve levels for forward colony bases. Prevents the scenario where you have to suddenly work out where all of Earth's fuel went and why it is 30b Km away 
I encountered the same issue, and while waiting for an implementation, I found a simple workaround.
Basically, I create a flow from Earth to a pickup base in orbit through a simple loop of orders and tankers/supply ships. This way, I can set the minimum amount of fuel and MSP to be stored in orbit, creating an emergency vault in case things go out of hand. Please note that I use SM to expand and create such orbital structure, and as I use it as a fix for a game issue, I don't consider it a cheat.
However, the downside is that it could still be vulnerable and potentially blown away. To enhance its protection, you can consider turning it into a ship and adding some armor layers, which would create an extra interesting strategic challenge in ensuring its safety.
It's worth noting that now I have moved a bit away from this and I try to tweak the routes to ensure they never exceed my annual production. It becomes challenging when you add another main HUB to Earth, and distributing nodes while keeping all systems operational becomes a fun and engaging aspect of the game for some.
I guess this is also more viable once the fix goes in to orders to transfer fuel/supplies to the structures so I can automate the resupply process. Still would have to wait till 2.2 though. How do you currently setup your orders with the structure? I originally went for structures because the capacity was fixed but the issues I had with automating it was annoying
Just refuel and resupply from the "ship" and loop it with a delay at the destination. Your problem is probably the same as mine where to "unload" from ship to ship it's not straightforward, which is why I have highlighted
"I create a flow from Earth to a pickup base in orbit through a simple loop of orders and tankers/supply ships". Basically, you have (Assuming Alphan Centauri as the new HUB)
- A Earth Colony - Earth Structure = which is route 1
- B Earth Structure - Alpha Centauri Colony = which is route 2
- C Alpha Centauri Colony - Alpha Centauri Structure = which is route 3
Ideally, you may use the structures as main nodes for all intra-system commercial operations.
With this system, you can have smaller liners doing the Colony Structure route only, or a bigger ship could do the whole. So if you pick up Fuel from Earth and load 10,000,000 litres, drop it at the Station and then pick it up again to drop it off at Alpha Centauri, assuming you do not have enough fuel and hit the reserve level, the ship will load only what is effectively available. You will still encounter the random bottleneck of ships going with just the bare minimum amount of fuel to do the round trip, which is why, as I said, recently I have been trying to understand what my actual intake per year of fuel and MSP actually is, prior committing to any loop of transfers.
The last time I used this method, I had a big dedicated ship to transport both Fuel and Supplies. I found out that capacity is more pressing than time, so it's not a fast-paced cargo. Since the arrival of
Riders you also include a commercial hangar for a couple of fighters in case of random encounters, however, it will make automation obsolete if you are "forced" to use them to defend your cargo.
