The new Mac Pros come with six Thunderbolt ports and one HDMI port, which all can be used for connecting displays to. These seven ports are separated into three buses, and when connecting multiple displays, Apple recommends using a separate bus for each (if connecting less than four displays) for maximum performance.
The bottom two Thunderbolt ports and the HDMI port all are on Bus 0. The top right two Thunderbolt ports are on Bus 1, and the top left two Thunderbolt ports are on Bus 2. See Apple’s documentation, including an illustration, for further details: http://support.apple.com/kb/HT5918