A method and apparatus for coating two sides of a single pane of glass or other substrate in a single pass through a coating apparatus. A sputtering line is provided, this line comprising a series of sputtering chambers. At least one of the chambers comprises a downward sputtering chamber having an upper target. At least one of the chambers comprises an upward sputtering chamber having a lower target. In some embodiments, the upper and lower targets are rotary targets. The coating apparatus advantageously has a plurality of transport rollers for conveying the substrate along the sputtering line. In certain embodiments, a majority of the chambers of the sputtering line are downward sputtering chambers each having only an upper target with no lower target.