@ OP
OKAY~ Finally something I can help with.
As far as I can tell, your SSBB can be loaded just fine through USB, but can't be "hacked" through the SD card like normal. you can activate the codes just fine, but you'll never get the textures to read.
However, if you use wii-scrubber, open up the brawl ISO, and go into the Data Partition, you'll find folders like you would place in your SD card (Fighter, system ,ect)
From there, you need to turn off ALL other programs while you do this (yet, even your internet browser) to prevent crashing.
You'll need to rightclick each individual file, click load, then navigate to your replacement file (I suggest sorting them out so as to help navigation.) The WiiScubber will replace the file, reload, and you'll have to navigate back to where you were to continue, repeat until finished.
Then make sure your codes are loaded into a folder at the root of your SD card called "codes" boot them with USBGX or NeoGamma (I personally use NeoGammaR8, hasn't failed me yet, and all my textures except two seem to work just fine, which I think was an error on my part because I used beta skins.) With cheats enabled, and you're off to the races
Otherwise, I have no idea on how to boot the game from USB and load from SD, I'd prefer that TONS over having to do this rig-a-ma-roar, but since my disk drive is busted, Gecko and riivolution arn't going to work for me.
(I should mention that I've only used this method for texture hacking thus far. I'm pretty sure stages and possibly system files can be edited this way, but I'm not quite sure about Character select portaits, ect.
Also, you'll want to backup your brawl ISO to another folder, copy it to another folder, and use the copy for hacking. Another problem is that once you save the hacked ISO, it compresses it somewhat, making it impossible for you to re-open the ISO and edit it, as far as I know. Meaning you'll have to re-do EVERYTHING if one thing doesn't work. xD (When I tried, my Scrubber bugged out on me D:)
(Again, I've only tried this with textures and personal experience. I'm no pro and you might have a better program for editing files like this, or a program that will let you re-open the files for editing later, and if so ,GIMMIE GIMMIE.