[TxMt] noob question: saving as projects

Forgive this really bone-headed question, but when I go to save a collection of files as a project -- and I have created them within the project using CMD + Shift + N -- both a project file is saved as well as the individual files. In other words, the individual files appear in the finder. Now, if the groupings were also being saved as folders/directories, it might be okay -- this is what happens when drags a collection of folders and files to Textmate. I thought the save as project feature produced a package of some kind? I don't see a preference I could have changed, so I'm wondering what's going on.