Applications should always be run off the Internal Driver and if possible the boot drive.
Internal over External
Internal PCI-E SSD over Internal SATA SSD
SSD over 7200
7200 over 5400.
Thunderbolt2 over Thunderbolt
Thunderbolt over USB 3.0
USB 3.0 over Firewire
Firewire over USB 2.0
Whenever I'm working on a project, that entire project is moved to the SSD, that is probably more subconscious reliability over actual reliability.
Once you start that program it's in memory, and more then likely even with a 5400 rpm you won't bottle neck the drive.
For anyone looking for an SSD newegg right now has a 256GB for $160. These things are diving in price.
Toshiba Q Series Pro HDTS325XZSTA 2.5" 256GB Internal Solid State Drive (SSD)http://www.newegg.com/Product/Product.a ... 6820168089
I bought the OptiBay for my old MacBook Pro that replaces the CD drive with another Hard Drive slot. http://www.mcetech.com/optibay/
So a 256GB SSD in the stock slot, then a 1TB drive in the CD drive slot.
Also I wouldn't bother with a Hybrid or Fusion over looking at two separate drives.
You don't want your drive or OS to determine what goes on the SSD and what stays on the Platters.
Unless you are using those files every day, it's not going to assume to move those files to the SSD section, because it not something you use all the time, which is what the Hybrid and Fusions do.
They look at the file/sectors being used most often(day to day) and move those to the SSD part of the drive.
With two separate drives you can say, "I want these files on the SSD and be crazy fast."
....just my 2cents.