Graham,
The autoupdate with the Y is for each individual aircraft and is to show whether to sync with the server or if set to N to leave alone as you have changed something in the record manually and want to keep it that way. To update the whole database each day, week or whenever you like you go to database explorer and update from there. Opening up database explorer now shows 2 tabs one of which is database updates and you have two options their either update everything or leave manually changed records alone. Once you have made your choice and pressed the Start Update button you will see a green line going across the bottom of the window to show the progress and once finished you will be advised to restart RB to finish the process.
In between these updates if you pick up an individual aircraft, if the autoupdate has been set to Y and any changes have been made to the data held in the server, that change will be applied, if set to N, any change on the server will be ignored.
Hope that helps
Alan