Xeon! As you spec'd out, you can have dual Xeons on your mobo. And AFAIK, the iX series doesn't support multiple CPUs — and that's essential for fast Cinema 4D rendering. The speedup is pretty linear for 3D. Dual 8-core chips are always to be faster than one 6-core for 3D.
However, neither of the GTX boards you mention is listed as Premiere Pro CUDA certified. (Just forget about CUDA on AfterEffects. Just don't go there. Pretend it doesn't exist.)
The Quadro + Tesla combo on the other station is complete overkill (at least for the apps you mention). So really neither station is optimal.
But any money you have left over, I would seriously invest in a SSD or two — as big as you can afford. An SSD as your system drive is simply breathtaking. And using a secondary SSD as an AE/PP scratch disk gives you phenomenal performance.
And RAM. Premiere and AE share a common pool of memory. So if you are running them both that once, you want as much RAM as you can reasonably afford.
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What Navarro said. Raytracing scales almost linearly with the number of cores/ CPUs and Cinema 4D should be your primary gauge for this. Navarro may have a point about that CUDA stuff, but if you only use Premiere 10%, it's a typical case of: Why bother at all? Normal OpenGL based acceleration will still work and for simple edits with just one or 2 tracks that's always enough - I can do that on my 6 year old machine even. And sincve you're gonna have 2 CPUs, a lot will be possible to offload to them. It may require rendering the timeline at times, but really, I'd consider it a minor inconvenience at best. Likewise, at this point the only plug-in that uses CUDA in Cinema 4D is Turbulence FD. They may be adding some stuff for R14, but that's pure speculation. In any case, C4D itself would only use one card for its OpenGL stuff. So in sumamry: Don't waste more money than you realyl have to. Getting those Xeons and a single 680 will be lots of juice. Rather get more RAM or a bigger SSD for the money.