The project file, the file that has the information of what clips are part of it, the sequence information, etc. is VERY different from the actual capture scratch, audio renders, video renders, etc. The project file itself is VERY small compared to the actual video files - you can place the project file anywhere (like in your Documents folder) but store the actual video files on a separate high speed drive.
In all honesty, there are two things you don't want to do:
Store your video files on your OS drive
Store your video files on a partition of the drive your boot partition is on.
Some of the reasons include:
If the OS needs to access the drive the same time you have certain video work going on (whether it be for memory swap, just accessing standard operating files, auto save a project, etc.), it can cause problems for the OS or working with the video, neither something you want to deal with - especially if you're every importing footage from tape.
Video scratch drives get thrashed, A LOT. This gives video scratch drives a higher chance of failure compared to normal OS boot drive. If you're working on video on your boot drive extensively, you run a higher risk of drive failure then if you keep the video on a separate drive for scratch. If the scratch drive is the same drive as the OS/boot drive, and it fails, you won't be a happy camper when your computer no longer works where as if a scratch drive fails that's separate, you may be angry, but your system will continue to work.
On any system that I edit with (whether it be the iMac I'm at right now, the MBP that I sold earlier this year or my Mac Pro at home) - I ALWAYS have my scratch drive be a separate drive (not just separate partition) from my boot drive.