does Project M use a separate title id? if not that is the first thing that needs to be changed, otherwise they will both share the same banner.
The banner in SSBB is in <Game Partition>/system/banner0.bin
it may be worth a shot to try replacing that with a custom banner, as it may just be a copy there, and the actual one that is written to the save folder is in another location (or archive)
The banner in SSBB is in <Game Partition>/system/banner0.bin
it may be worth a shot to try replacing that with a custom banner, as it may just be a copy there, and the actual one that is written to the save folder is in another location (or archive)