I know just enough to be dangerous...that said I had Power Commander a module on my last Harley. I hooked the whole mess up to my lap top while the module was on the bike an tuned the electronics for more HP and also richened the fuel mixture. That with a Stage I kit and some other simple mods made for a pretty hot, pretty much stock 88ci Twin Cam FLHRCI.
Not sure if this is germane to this discussion, so take it in the spirit that it is given.