You may switch to release 1.2 (latest stable release and more recent than 1.2b6) or 1.3b2 (newest beta release), I would suggest 1.2 if you don’t need any of the new features of 1.3b2.
In any case, as Raja said, second SD slot is supported since 1.1b4 release.
In terms of GPIO configuration:
you don’t need to set the direction for the pins, when they are connected to SD controller this will be managed automatically by the SOC
For CD and WP pins (174-180) the alternate function is GPIO (5), but you have to configure those pins in a different way, described here: Windows Embedded Compact - iMX6 BSP Release
(will move that to knowledge base to make it more visible, sorry for this)