The GPUs consumes around 20-35% of their power from the PCIe slot, and the rest from the 8-6pin connectors, therefore if you put all risers in one PSU and the rest on the other PSU, the load between them will be quite unbalanced.

The best would be to use 6 GPUs (both top connectors and risers) + motherboard in one PSU and the other 6 GPUs in the other PSU. Also make sure that the PSUs are below 75% load as philipma1957 suggested.