What is it being hooked up to? I would recommend the DVI port, as that is what most monitors have, and it is just a little better than VGA, especially at high resolutions. HDMI also attempts to carry sound, so if you use that, you would probably have to redirect your sound signal to wherever. But either way, hook your displays up to your card, and not the MoBo.
The only advantage of using HDMI over DVI is if you have integrated speakers into the display you are using, otherwise if it is a regular monitor, without speakers and is up to 1920x1200 resolution it does not matter which of them you are using.