beeing able to set two different folders, one for incomming and one for outgoing crafting would indeed a very good idea. especially when you think about multible crafters in one corporation. so you can keep the resources in the corp storages. now you have to split them up and it happens all the time that one or more person runs out of at least one commondity.
this would greatly improve gameplay.

simple solution:
every corp can set a incomming and outgoing corporation folder. where that is and under what security that is up to the corp itself. if you have the roles you just right click the folder and set to incomming or outgoing production folder.
players can do the same for their own personal use.

at production screen you can use the already existing check window for corporation production or just add a second field for that. (important: pls save the last used setting to agent so you dont have to redo it all the time)
this will then decide if your private or your corporation folders will be used (if you have the propper roles and access levels!)

[p.s.: and dont forget to add a reset to default option! ]