Yep, np. I just checked again and you're right, the manual doesn't say the first is degraded to x8 (my P5Q-E manual is probably very similar), however, its a limitation of the P45 northbridge chipset, which only has 20 PCIE lanes. When the 2nd slot is used the x16 link is split into 2x8 for the first two slots.
As for the graphics card, I wouldn't worry about it as a 2600XT doesn't require full x16 bandwidth to function at capacity. Also, your Areca is actually x8 physical, so its also x8 electrical link max, so you'll be capping capacity in that 2nd black slot at x8 electrical.
I'd go ahead and put the Areca in the first black PCIE slot, giving you 4 GB/s bandwidth, which should be sufficient for even 12 SSD in RAID 0. 2GB/s might limit you marginally, however I'm pretty sure I've seen benches of SSD RAID arrays hitting STR of ~200MB/s each, so 12 of those could theoretically break the 2GB/s bandwidth offered by an x4 PCIE slot.