What's the best way to configure my thunderbolt drive with the new mac pro?

I have an external pegasus drive connected to my mac pro.  Obviously the computer is limited in space and I was wondering whether I should move my "user" folder which will include documents, pictures, videos, etc onto the pegasus.  That way the 256gb hard drive on the mac pro is dedicated solely for the os and and apps.  What do you guys think?

I concur. See the following:
How to use an SSD with your HDD
If you are going to use an SSD as a boot drive together with your existing HDD as the "data" drive, here's what you can do.
After installing the SSD you will need to partition and format the SSD using Disk Utility. Then, install OS X on the SSD. After OS X has been installed boot from the SSD. Use Startup Disk preferences to set the SSD as the startup volume.
Open Users & Groups preferences. Click on the lock icon and authenticate. CTRL- or RIGHT-click on your user account listing in the sidebar and select Advanced Options from the context menu.
You will see a field labeled "Home dir:" At the right end you will see a Change button. Click on it. In the file dialog locate the Home folder now located on the HDD (HDD/Users/account_name/.) Select the folder, click on Open button. Restart the computer as directed.
When the computer boots up it will now be using the Home folder located on the HDD.
Another more technical method involving the Terminal and aliases is discussed in depth here: Using OS X with an SSD plus HDD setup - Matt Gemmell. This is my preferred approach because I can select which of the Home's folders I want on the HDD and which I don't want. For example, I like to keep the Documents and Library folders on the SSD because I access their content frequently.
Be sure you retain the fully bootable system on your HDD in case you ever need it.

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