Okay I think I understand now what you were asking. You don’t need two routes to one factory. Think of it more like a permission than a delivery order. If you have a routing order from storage for 3000 units of raw resources then the production plant will refill it’s storage from that source as long as that resource is available.
On that note extractors should always be routed to a buffer, for smaller operations that’s going to be your spaceport which doubles as storage. Otherwise directly linking an extractor to a T1 factory will cause the loss of any resources which overflow the factory’s internal storage.
And yes you are correct. Extraction cannot be edited while a program is running. You will need to stop the program first and there is a waiting period after a program is started before it can be stopped.