You can do it using GCTedit.
It should be easy enough to use... But I have never actually used it myself so I can't be very specific 
the issue with gct eit is it's good for adding new codes but it's a pain to take them out it has very little in its database so most codes come up as a huge wall of numbers labeled as unknown codes, if it's from the B+site they usually have a .txt form of the code find it and open it in notepad look thru and there should be a code in there affecting the stage, simply delete it and use code manager or brawl+ tweaker (what i use) to make a new .gct with the .txt file.
i would keep the .txt file for easy code adding/deleting.