Replacing Ships: When managed ships are destroyed, the manager will attempt to replace these, either by buying from a local shipyard or ordering them from your headquarters, if you have the necessary blueprints. If the manager is unable to replace the ship within a reasonable time-frame, the replacement will be cancelled and you will be notified.
Repairing Ships: When managed ships are damaged, the manager will send them to a local shipyard or to your headquarters for repairs. The shipyard or HQ must be within the station's jump radius, and there must be sufficient funds in the station account for automatic ship repair/replacement to function
Supply Stations: You can add you own stations as supply stations for the Station Manager to use. The station manager will then pick up the products from that station when it needs them instead of buying them from other stations. The manager will also deliver resources if needed. When picking up or delivering to supply stations, no money will change hands, so acts as a free transaction
The Station Manager Restrictions option, also available in the station's command console, allows you further control over what the Station Manager is allowed to do. It can be used to specify wares that should not be bought or sold, to ignore certain ships to prevent them from being used by the Station Manager, and to blacklist sectors. Blacklisted sectors specified here are in addition to those set globally.