The 2 red slots are PCIe 3.0 and its lanes are derived from the cpu. You cannot change this. It is manufactured as such. Being from the cpu, the maximum number of PCIe3.0 lanes are 16 for ONE gfx card, dual gfx cards will be x8 EACH. Your manual and mobo specs confirm this fact.
Note: 'Dual' in the manual does not mean the second card per se. It means two cards occupying the two slots. Therefore the description 'x16 or dual x8, red' in the manual. Read the proper way, the description means 'single at x16, dual at x8 each, red slots'.
The black x16 slot is PCIe 2.0, meaning the lanes are derived from the PCH (Platform Controller Hub), i.e. the Z87 chipset, not from the cpu.
[strike]So if you want both your cards to run at x16, put one in the top RED slot, and the other in the BLACK slot. However, the one in the RED will be capable of about double the throughput of the one in the BLACK slot - the difference between PCIe 3.0 and PCIe 2.0.
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There is no such thing as VGA Gen3. PCIe 3.0 is sometimes referred to as Gen3, and PCIe3.0 as Gen2 - 'Gen' meaning 'Generation'.
Edit: There is no way to run 2 cards at x16 with this motherboard. The Black x16 slot, though PCIe2.0 is limited to max 4 PCIe2.0 lanes, default setting at x1 lane (so to get 4 lanes, one needs to specify in the BIOS). This info is derived from the footnote in the specs -
"*1: The PCIe 2.0 x16 slot (PCIEX4_3) supports up to x4 mode. It shares bandwidth with PCIe 2.0 x1 slots. The default setting is x1 mode."
yeah I will try that later when I get home. the MOBO should run the first card as x16 and the 2nd as x8. ive checked the manual. 
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