The first question is around my fuel refinaries - I take a ship design with loads of fuel capacity and a bunch of sorium harvesters. I set it as a "tanker" so as to get the "unload 90% option. It's default order is to move to a gas giant with sorium and harvest until full, then to return to a colony and unload 90% of the fuel. Which almost works. What seems to happen is that a newly created ship will unload to 10%, move to a sorium gas giant, mine until full, and then refuse to move to a colony and unload. I think I am doing something wrong but I can't for the life of me figure it out.
The newly created ship only loads 10% of its fuel capacity since it is listed as a tanker. I don't use the default orders. I just wait for it to have harvested for a year, then manually give it the following orders: "Move to colony", "equalize fuel percentage at colony" and "unload 90% of fuel at colony." As a typical harvester group has 3 ships this leaves them all with the same fuel. This works fine frankly as it is something that I have to do only 12 times per game year. I don't know why the default orders don't work exactly the way they should. Personally outside a few of them I find most of them aren't worth using.
After it unloads I leave it for shore leave for a few weeks and then give it a order to return to the gas giant. I get warning most of the time by Fuel Harvester at 90% messages so it isn't something you have to invest a lot of care and attention to.
The second question regards civilian sorium harvesting operations. Do they sell the fuel to me (ie does my stockpile increase)?
You send a tanker (or other ship) to the civillian ship and give it the "refuel from target fleet" order. It will then take fuel from the civillian harvester and you will be charged for it. Every few months I do this to skim off the civillian production. Their harvesters are a god send as the price you pay for the fuel is chicken scratch.
The last question is about sorium mining (as opposed to fuel refining). Because it's used for jump drives etc, I don't want all of my actual sorium reserves refined into fuel. So I set a reserve on the level. And it's ignored. Is there a way to not refine sorium (other than shutting down refineries)?
No there isn't. If you want to not refine your sorium you will need to turn off your refineries. But really you should have loads of sorium in your stockpile and the amount you need for ship construction and maintenance is fairly minimal so I don't see where this is a problem. The reserve level isn't ignored, but it is only valid for cargo loading operations, when you give a load all minerals command the ship will only take those minerals above the set level. It doesn't prevent you using the minerals.