Maybe it’s clear this way:
For every 2 lanes you want allocated to the PCIe slot (up to 4), you lose two SATA lanes. Since there are 8 lanes total, but 12 possible lane destinations, they pre-made combinations of destinations that they think would be useful:
- All 8 lanes to SATA, 4 onboard and 4 through MiniSAS
- 2 lanes to PCIe and 6 to SATA, 2 onboard and 4 through MiniSAS
- 4 lanes to PCIe and 4 to SATA, either activating the 4 onboard ports or the MiniSAS (but not both)
To use DOS-based flash tools, you must boot in BIOS mode with CSM (and OPROMs too, I think) enabled. If you’re booting without a CSM, use an EFI shell with the EFI flash executables.