This should help you get a better understanding of the HD5870 cooling system;http://www.xbitlabs.com/articles/video/display/radeon-hd5870_6.html#sect0
Part of the air leaves through the exterior, outside the case, and the other part leaves through the small slits at the top-back of the card (back being towards the rear of the case).
As for the difference with the fans; you'll be having 'cool air' being blown on top of the most heated part of your system, of course it'll make a difference. However, you might want to experiment with different fan configurations to find an nice and happy medium. Ultimately, I'd say that 85-90c max is a good temperature for an mATX case.