Keeping things simple, as the existing vessel / proposed design in question is unknown, free-surface effect can be greatly reduced by.... Dividing a larger tank into smaller ones, the divisions running fore and aft. Keeping the tanks as close to full as possible. Positioning the tanks as close to the longitudinal centreline of the vessel (as far inboard) as possible. Fitting longitudinal baffles to the tank. An additional note for multiple tank layouts, would be to design the fuel / water system so that the furthest outboard tanks are deplenished first, if the tank layout allowed this.
One should also burn off one tank at a time if possible rather than ending up with all tanks half full.