ok so these boards are not even standard atx motherboards and i am assuming you are talking about developmental boards, or special usages ones.
Next question did you read the manual where it said that the 2 boards can be connected via the port that looks like a pci-e port?
If you just need a direct connection, you may be in trouble as i have never seen a pci-e riser with both male ends. That is what you need to look for, a pci-e riser with both male ends.
Now if your thinking you can plug in 2 pci-e express slots to each other on different STD PC ATX boards, then no. It does not work that way as Elf states and infact doing so will most likely end up frying the pci-e ports on both boards.
Can you take a picture with your smart phone.
Post the picture on a free image hosting site and then post it in this thread for us to help you out?