You should get a liquid cooler for the card whose air flow is being blocked.
If you have newer and faster cards you need to put them in x16 slots running at x16 speeds. Or your card will be bottlenecked by the slot.
The motherboards I mentioned in my earlier comment has 3-4 PCIE slots but not all work at x16 mode. Some x16 slots have have only the number of pins required for a x8 or x4 slot. Hence these are called x16 slots running at x8 or x4 speed.
http://www.newegg.com/Product/Product.aspx?Item=N82E16813157343
This motherboard has 3 PCIE 3.0 x16 slots running at x16 speeds and 1 PCIE 2.0 x16 slot running at x16 speeds. But it's price is almost £250-280. So you are better off with a liquid cooler GPU setup which will cost you about £50-80.
Since you are going to cool both the graphics cards you can hook them up with the dame radiator hence decreasing the cost.