Identifying bottlenecks In any computer, there is a bottleneck. The processor, the amount of memory, the bus to the hard drive, etc.

I just ordered a 2010 MacPro, 12 core, and although the 12*3.33 GHz cores should give me more than 3x the performance of my quad 2.8 GHz, I understand it probably won't. I am wondering what the weak link will be and how to improve it. The first thing I'm considering is a PCI card with 2 SSD RAID 0 to run the OS. On my old Pro, I saw amazing boot times from a shift to SSD. 
The Mac will have 32GB of RAM, I'm assuming that's enough. 

Update - One example of an intensive process is video encoding. How do I find whether writing to the hard drives is the slowdown, i.e. that raid 0 for the hard drives would help the speed? 

Any other advice? How do I identify the bottlenecks once this machine is running?
OP I think you're looking at the problem a little backwards. Your weakest link will inherently be the I/O bus.
That being said, raid-0 on PCI-e SSDs will be quite performant.

You need to ask yourself a couple questions


What are you trying to optimize for? Its a mac pro and you're cosnidering a significant $ investment, so you're probably doing some professional work. Keep in mind though that you're sinking a lot of money into a 5+ year old machine, and the parts won't be reusable on any new mac pro you buy in the future
What are your pain points now? You just ordered this machine, so you haven't actually used it yet as part of your workflow. Firstly, you might find it more than adequate for what you want to do. But currently, what are the things you are struggling with? We can help answer from there.