First we must know the serial number on the twilight princess disc, so we can use the correct save file.
Using sdgecko does change the version of the twilight hack you should be using- but if you already have the homebrew channel installed you shouldn't need to use the twilight hack anymore.
Have you injected the smash bros rom into a vc wad? because if you have I don't think we're allowed to talk about that here and I'd recommend looking eleswhere for a solution. If you're just using a smash bros rom I don't think it will work with wad manager alone, I would wait until a better N64 emulator is made.
Finally try to boot other homebrew with the homebrew channel and see if it works correctly, and also see if wad manager will install other .elf files as channels successfully.
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