There are, to my knowledge, 2 ways to handle extractors.
1. Put engines on the extractors and when they are full, have them return to a colony or fuel storage location and unload their fuel. Repeat till the planet is out of Sorium.
2. Do not put any engines on the extractors. Tug them into location. Build a tanker/oiler type ship that is marked as a tanker. Give it a queue of orders that will tell it to go to the extractors, fill up on fuel, and then go to the colony or fuel storage location and unload the fuel. Mark the queue of orders to repeat, and you are all set. The only time it needs to be modified is when the extractors need to be moved to another Sorium source.
To me, #2 is more efficient, because the Extractors can be built very large, like you have done, and you do not need to add engines to it which will be rarely used. Also the tanker/oiler will be useful for a number of other purposes. I build mine in the 9K to 12K ton range so that they can move fuel to where it is needed, service my military fleets, and help rescue the occasional ship that runs out of fuel.