Looks like there will be some interesting technical possibilities in the upcoming DirectX 12. Based on an anonymous source, Tom's Hardware reports some interesting details about the way multiple GPUs will work with DX12.

Currently the most popular way of using SLI or Crossfire is to mirror VRAM contents on both graphics cards and render alternate frames on each of them (AFR). This method is relatively "simple" to implement and can often nearly double the average framerate. It also has several important disadvantages. The time spent between capturing player actions and displaying them on screen is not reduced, so getting 60 FPS while using AFR leaves you with the same amount of lag as 30 FPS on a single GPU. The variable amount of time it takes to render different frames is more apparent in AFR mode, giving more micro stuttering. Finally, VRAM on additional cards only mirrors the contents of the first one, instead of adding any additional video memory capacity.

Based on the current rumours, DirectX 12 should combine all available graphics resources in a given PC into a single pool with precise control over them. DX12 should make split-frame rendering (SFR) easier to implement than in previous versions of the API. With SFR, each GPU takes over rendering part of the frame, thus reducing latency compared to a single GPU. There should be some automatic tools available for developers to implement SFR. However, it is very likely that additional effort beyond the automatic will be necessary to implement well-working SFR without visual artefacts. This seems very promising, considering that Civilization: Beyond Earth already uses SFR in Mantle mode and it works very well.

Finally, all available graphics resources means just that – all. Thus, in a PC with GPUs from different manufacturers and different architectures, all of them will be available at the same time via DirectX 12. From a technical standpoint, it will likely allow GeForce card(s) to draw a part of the frame, while Radeon draws another. Graphics vendors' driver blocking attempts notwithstanding, the simultaneous use of such extremely diverse configurations will likely remain the stuff of tech demos. Implementing these features requires a lot of developers' work and can introduce many bugs. Therefore, games will likely still only take full of advantage of multiple GPUs using same architecture.