So I think what you're alluding to is that although Gnome Shell presents a version of the "Applications" menu, it doesn't (AFAIK) present the "System" menu anywhere.

So, you have to add a launcher for the tool you want to run somewhere in the Applications menu tree.  That's easy but not trivial:

 1. click on your name up in the upper
    right hand corner
 2. click on "System Preferences..."
 3. click on "Main Menu" in the
    Look-and-Feel section of the
    "Control Center" that pops up
 4. select the section where you want to
    add the software-center launcher - I
    chose "system tools"
 5. click the "new item" button
 6. enter "software-center" as both the
    name and the command 
 7. click "ok"
 8. click "close"

Now when you select "Activities" in the upper left hand corner, then the "more" button just to the right of the word "Applications", you'll see your new software-center launcher listed in the system tools menu.  

I tried this and it worked perfectly.<br>-pbr