PCI-e + SLI?

That's the board.... where? how? do you even say that it's NB is blocking the PCIe Slot?

If it's the PCIe x1 slot then yes for some cards that may pose a problem, but they are compatible with the Slots right down the board.... only the size is larger, doesn't mean you can't stick the PCie x1 Card in the PCIe x16, x8 or x4 Slot.

The Xonar
System Requirements
One PCI Express 1.0 (or higher) compatible slot for the audio card

I think it is safe to assume that you'd be using 2x 580GTXs in slots PCIEX16_1, PCIEX16_2
Which still leaves you with 1 x PCIEX8 and 1x PCIEX4, if you use the PCIEX8 then you'll loose speeds in the PCIEX16_1 but I don't think that will be accessible due to the 580GTX being a double slot card. So it's safe to assume that you'll use the PCIEX4 slot for the Xonar.
And yes, it will work.
If you feel that the Xonar might cause the lower card to heatup due to it being so close to the heatsink of the lower 580GTX then you can always buy one of those PCIe Flexible Risers and just Lock the card onto another expansion bay in your case away from the card.
http://www.amazon.com/PCI-Express-Riser-Flexible-Cable/...

That is the older UD5, I am talking about the 990FXA UD5 found here...

http://www.newegg.com/Product/Product.aspx?Item=N82E168...

Ok, in that case, you will be using the PCIEX16_1 & PCIEX16_2 Slots for your 580's, leaving the PCIEX4_1 & PCIEX4_2 inaccessible due to the GPU Heatsinks right.
That leaves one PCIEX8 Slot accessible and can use the Xonar in it.
It is again a full length slot but it is compatible with the card.

Or you could use a PCIex1 riser running all the way to the bottom from the PCIEX1 slot next to the NB, but that would be a waste since the card and the PCIEX8 slot are compatible....
Only problem is going to be cooling the GPUs both cards will not have too much space between them and the Xonar once plugged into the last PCIeX8 slot will also leave very little room for air to the 2nd GPU.....That would be the only worrying factor, IMO.

So that would leave you with the 2nd GPU running at 8x  
Maybe using a riser from the first or second PCIEX4 slots will do the trick. The flexible ones will fit in without causing a problem for the GPU Heatsinks and can easily run across the board without a problem.
That way you'll still have SLI with both cards running 16X and the Xonar working too.