Crews will try to fill buildings with resources from all available storage bays nearby, even from other ships. Also add a storage priority designation, so crews will try to move resources from generic storage bays and designated storage bays with lower priority to storage bays with higher priority. Crews do so only if both ships are stationary, or they will only transfer resources in their own ship instead. This should make the game easier by reducing the need of player manual resource management between ships.
For example, if you designate a storage bay in an industrial ship A to store ammunitions with priority 8, and a combat ship B with cannons and/or storage bays designated to store ammunitions with priority 10, so long both ships are stationary and in resource transfer range, your crews will automatically start to transfer ammunitions from ship A to ship B, until the latter's cannons and designated ammunition storages are full. Further more, if ship A has storage bay that is designated to store steel, your crews will also transfer those steel that ship B possibly received by salvaging from ship B's generic storage bays into ship A.
When it comes to mining and salvaging, crews should move the resource they picked up to the buildings in need, even the buildings are not in the ship they are from. After that, designated storage with highest priority. And finally generic storage bays. So your combat ships without any storage bay can still help salvaging enemy ships as they will transfer the materials to your other ships with spare cargo space.
This should make it a viable choice to separate ammunition production from combat ships. If you do so in current build, it requires a huge amount of player micro management to manually transfer ammunitions from one ship to another by mouse clicks. Also it becomes possible to build DIY space stations which supply your ships and receive minerals and ship debris from them.