If you need to go with the two psus, I would power the board and the first few GPUs with one PSU and the rest of the gpus with the 2nd PSU. I have done this before and it works. If you are using psu's that can be synced like the Antec HCP, hook up the sync cord so they both turn on and off together. Alternatively, you need to make sure to turn on psu 2 then psu 1. When you shutoff, do it in the opposite order: 1 and then 2.
this is the way i have my onda d8p (a similar mobo), all mobo connections and a 2-3 gpus on one psu, and the remaining gpus 6/8 pin connectors on the 2nd.
i used a add2psu (a relay) to control both psus from the motherboard power button. makes it easier as you dont have to worry about the order of psus turning on/off. not strictly needed though.
Sounds like a good working solution. I wasn't quite clear on one part of your description. If your GPUs have two PCIE connectors, both connectors from each GPU should be hooked to the same PSU. I believe you described it this way but I wasn't quite sure.