I have done some research, the kernel looks like it has PCI enabled in the config (how/if it's implemented I do not know) and I'm now leaning toward u-boot needing some configuration to use the PCIe bus. I have reached out to support but no reply from them at this time.
I did just get confirmation on the #linux-rockchip irc channel that someone has actually gotten pci working but not with the firefly. He pointed me to the https://github.com/rockchip-linux/kernel project and said the 4.4 kernel is what he used. He was also kind enough to show where in the device tree pci was defined https://github.com/rockchip-linux/kernel/blob/release-4.4/arch/arm64/boot/dts/rockchip/rk3399-firefly-linux.dts#L744 Now, last time I looked through the firefly SDK source and compiled a kernel I did notice that device tree was not enabled in the .config so unless I misunderstood something, the kernel will need to be compiled with device tree support to properly use the pci bus. This should include m.2 SSD devices also.
