I am new to FCP and have a question on Project Folder location vs Media Location.

From what I am learning on Lynda.com they say to put the Project Folder on the System drive and Media on a different.

I have three internal drives.
System drive with OS X and all Software 250GB

Internal One with FC Auto save and Project Files 750GB

Internal Two with After Effect projects, Digital Juice, Smart Sound, etc.750GB

External RAID with Final Cut Pro Documents. 4TB

Does this make sense to have the projects on a different drive then the OS and software? I do not want to run out of space on the system drive over time and have it run slower.

That's perfectly fine, whatever floats your boat.
I always keep my project files separate from my autosave just in case one goes bang and always back-up critical data. With that amount of hard-drive space you should be able to back-up your back-ups!

Thank you Liam.