You won't be able to assign more cores to AE until you add more RAM. Explanation:
1. AE requires that you assign 2GB of RAM to background processes. Therefore, on machines with 12GB of RAM (like the two you have), there would only be 10GB available for use. There's no way around that.
2. AE treats every logical core as a physical one. So, a hex-core machine would appear as 12 cores to AE and a 12-core machine would appear as 24. AE needs at least 1GB of RAM, PER core and preferably, you'd want at least 2GB per core if you're working with large compositions. And this is exactly why AE will only allow you to assign 10 cores (with 1GB of RAM each) on both machines. 2GB of RAM to the background and 10GB to AE, totaling your 12GB of installed RAM.
In short, AE is a memory pig. Assuming you'd want 2GB per logical core assigned to a hex-core Mac Pro for rendering, you would need at least 26GB of RAM. 12 threads at 2GB each, plus 2GB to background - and you would have to double that figure to get all 24 threads working the same way on your 12-core.
If upgrading RAM isn't an option, it's very likely you that you'll get better performance using less cores, but with more RAM assigned to each. That's been my experience with 64-bit AE, anyway. I have 16GB of RAM (not going any further on this machine because the FB-DIMMs that 3,1s use are too expensive) and I have AE set to 6 cores at 2GB each, which is notably faster than telling it to use 8 cores at 1GB each. But YMMV.