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Never run homebrew through the supercard patcher.  The supercard patcher software is for commercial roms only. (at least for now)

Most homebrew will come with .nds and .ds.gba files.  The .nds file is the original homebrew binary, and is good for running with emulators, WiFiMe, and sometimes moonshell. The .ds.gba file is the patched version to work with a passthrough device (passme) and a GBA flash card.  The confusing part is supercard wants GBA roms to be named .gba, and NDS roms to be named .nds

With supercard the solution is to rename .ds.gba files to .ds.nds and that will solve most problems with running homebrew.

NDSLoader.bin is the program header that is combined with an original .nds file to output a patched .ds.gba file.  Sometimes you will need to manually patch a program if the hombrew only comes with an .nds file.  Supercard users should type the following at the command line "copy /b ndsloader.bin + [homebrew name].nds [homebrew name].ds.nds" (for more information search for ndsloader.bin)

Another confusing thing is that some homebrew will already come patched and will already be named .nds for use with supercard.  So if the homebrew doesn't come with a .ds.gba file you might need to experiment a little.  Some developers have started using the .sc.nds file extension to avoid confusion.