It should only be necessary to make one black wire connection to the negative wire from the control box, and I would suggest you connect it on the side of the ammeter that is furthest away from the battery?
Unfortunately I don't know what other changes have been made in order to upgrade to 12V as some wiring changes would be necessary, such as the need to join the correct two of the three alternator output wires together, the third lighting output wire also has to be re-routed, so I can't comment on the apparent ammeter discharge indication, without knowing more about how the electrical system has been altered?.