Oooh I see what I did wrong before when I booted GeckoOS directly. It was just the boot file, not in the folder with the other stuff in it. Herp.
Also on not always file replacing, I found that whenever I started regular Brawl either before or after playing Brawl+, then going back into Brawl+, it would fail to load the new graphics and everything. Restarting Dolphin solved it. I don't know if starting other games can cause it as well though.
Also on not always file replacing, I found that whenever I started regular Brawl either before or after playing Brawl+, then going back into Brawl+, it would fail to load the new graphics and everything. Restarting Dolphin solved it. I don't know if starting other games can cause it as well though.