The mini-pcie slots on the top of the board can be configured to be either SATA or PCIe. This configuration does not auto-detect yet and needs to be hard coded in u-boot. I can add a u-boot env variable to switch between them. You need to modify the #if 1 to #if 0 in the following two places –
https://github.com/SolidRun/u-boot-armada38x/blob/u-boot-2013.01-15t1-clearfog/tools/marvell/bin_hdr/src_phy/a38x/mvHighSpeedTopologySpec-38x.c#L92
and
This will modify the SERDES of the PEX (pcie) to become a SATA port
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