ControllerRemap is basically just a file rewriter.
Check my sig for a link to the full thread, the download is there and there's a full PDF that documents everything.
But basically, it's a purely command line app (no gui at all).
You run it BEFORE starting mame, so typically, you'd create a "StartMame.bat" file, and in it, run controllerremap, and then start mame.
For instance you might have a bat file
REM Start of file
ControllerRemap /Remap:c:\mame\ctrlr\MyArcade.cfg
Mame %1 –ctrlr MyArcade.cfg
REM End of bat file
So the idea is that the front end would start the BAT file and pass it the name of the ROM selected.
That would get passed in as %1, ControllerRemap would run, read and then rewrite the MyArcade.cfg file
and then mame would start and load that cfg file.
Like I said, though, LEDBlinky tends to want to read the CFG file only once, when it's first started, so that was something Arzoo has been looking into.