I just want to check that you're talking about the Logic 8 file... not "folder"..?
Once you install the upgrade for Logic 9, you'll find Logic Pro.app in your Applications folder and the previous version (Logic 8 and Mainstage 1) will remain there untouched.
If you wish you can delete the older application versions. However, if for some reason you ever want to use Logic 8 or Mainstage 1 then it might be a better idea to back these up.
Remember that when you perform some software updates for Logic (upto 9.1.x I believe) the older application version will be renamed from Logic.app to Logic Pro 9.0.app (or whatever the previous version number was.)
The most up to date application file will always be named Logic Pro.app.
Hope that helps