the n64 auto inject is just an application that was made to use injectuwad by creffca to make n64 injections instead of you having to type it out manually. If you want SNES then instead of clicking the n64injector.exe open up command prompt and do it manually.
injectuwad.exe romname wadname
Press 1 for SNES
it'll open up wadtool, click decrypt and find the wad you're using, after its finished close it
Now it'll ask "Possible Rom found Inject? y/n" hit Y
Now it'll bring up bannertool. Select open, 000000.app and change the channel names to what you want and hit save
now close the banner tool and it should finish up by itself and you'll have a wad in your folder named title.wad