The 'upper' port is the primary....
It's a Dual-Link DVI-I, which you can use for analog connections and 4K resolution connections, unlike the bottom which is just a Single Link DVI-D.
1 x Dual-Link DVI
1 x HDMI (with 3D)
2 x Mini-DisplayPort
1 x Single-Link DVI-D
Equipped with the most popular Dual Link DVI (Digital Visual Interface), this card is able to display ultra high resolutions of up to 2560 x 1600 at 60Hz.
Supports Digital monitors up to 1920x1200 resolution.