Hi Cloudy & welcome to the forums!
In Logic 7 I'd always recommend saving as a project and including all audio files, and settings if necessary within the project folder...
That's important, so when you back up your important projects and come back to them one day in the future all the audio files, exs settings, etc will be there for you in the project folder.
What I do, in terms of keeping the projects more organised, is to use folders and sub folders - often i use a date system e.g.
as the folder hierarchy. Then the project's prefix is a date follwed by the name of the song (073108_*name of song*).
This makes it very easy to find stuff later.
Also, if I'm working on a project I'll back up or save the projects to that folder, with a sub folder named after the project.
Hope that helps,