The dual gtx's dont split the line on higher end cards. Also, PCI-E 2.0 is not fully utilized in any configuration right now, so dont worry about that.
Basically your question is is there a difference using the 2.0 or the 1.0 slot with SLI. The answer is no, because the bandwith of ether is not split in SLI (because the board is high end) and because the bandwith of a PCI-E 2.0 is not needed when running a gpu, its just for future cards with higher bandwith.
And you want to use the top 2 because the SLI bridge only fits between them. Thats fine. Again, there will be no performance drop using the 1.0 slot over the 2.0 slot.