Hi tom,
Please refer to Chapter 42 (i.MX 6 PCI Express Root Complex Driver) of "i.MX_6_Linux_Reference_Manual.pdf" in Linux documentation. Also You may try using the recent (L4.1.15) Linux BSP.
The following thread may be useful. “i.MX6Q PCIe EP/RC Validation System”
https://community.freescale.com/docs/DOC-95014
When building RC image, make sure that
CONFIG_IMX_PCIE=y
# CONFIG_IMX_PCIE_EP_MODE_IN_EP_RC_SYS is not set
CONFIG_IMX_PCIE_RC_MODE_IN_EP_RC_SYS=y
* When build EP image, make sure that
CONFIG_IMX_PCIE=y
CONFIG_IMX_PCIE_EP_MODE_IN_EP_RC_SYS=y
# CONFIG_IMX_PCIE_RC_MODE_IN_EP_RC_SYS is not set
Hope this helps