I think I had looked everywhere, trying to find settings that apply/create for both ways.
Right now it seems to that you have to apply for only one route at the time - in the previous version, I think that there was a button called "Apply for return also"?
Inventory management for the route pair and flight number management for a particular flight look very very similar, you have to make sure you are in the Inventory... because these options do appear only in Inventory, but not under an individual flight number management.