Don't use a Y cable at all, since a Y cable takes output from one connector and splits the same output to two. This card has multiple connectors that each operate on its own. Use one for one screen, and a second unused one for the other.
It looks like different versions of this card have different connectors. Some have DVI only connectors (at least two), and another I saw has one DVI and two display port connectors. If you have the DVI + display port version, get yourself a display port to DVI (or display port to VGA if needed) cable instead of trying to use a Y cable.