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Ask your salesperson.
Well, I can try to help...I configured the beefiest Mac Pro I could come up with, then used those specs to build my own PC (running Vista, naturally) and from the PC side, I can tell you this...
- Buy as much RAM as you can use. On the Mac, I don't know how well the 64-bit stuff will work in Premiere and AE. On Windows, it's optimized for Vista 64 and it makes use of plenty of RAM if you have it.
- Don't choke the processors. You'll need at least 2 GB of RAM per core to really make the most of your processing power. Of course, if you're only running 32 bit compatibility, you won't really be able to make complete use out of "all" the RAM.
- Storage...well, it's difficult to say. You really can't have too much, but at the same time, if you're not editing uncompressed SD or any of the various flavors of HD (except HDV, which is the same as DV rate), you don't need humongous amounts of storage. Redundancy is good for your projects/backups and all, and RAID 0 is good for your media files (as long as they can be reclaimed in the event of a failure). Mainly, I would suggest getting or configuring an external RAID array and running it through a nice eSATA-capable RAID controller. Buy a single drive to run the Mac OS on and house your documents, and another one to house your projects, and one more for various production assets and captured/ingested media. Expand that as your needs increase and spread the costs out over your jobs as they come along.
- Processors...keep in mind how much RAM you can afford and try to balance the total number of cores with the total RAM available to feed the procs. 2 3.2 Ghz cores on a single proc are generally better than, say, 4 1.8 GHz cores on 2 procs, but that can depend on how many total applications are running simultaneously, and whether any or all of them are capable of using multiple cores and/or procs simultaneously.
Hope this helped (rather than add to your confusion). Good luck!
Buy the base Mac Pro, then add hard drives and memory from a qualified third party supplier. You'll save a ton of money and avoid the very hefty premium Apple charges for them.