The "subliminal" message technique i know works mixing a very, very low volume message with a normal volume music. You are not supposed to discern the message easily, but you HAVE TO hear it. It is like people not used to listen to encoders artifacts, they are there but they haven't noticed... And yes, if you concentrate enough, you may pick the message. Turning the volume real loud helps too, to know if its there or not. There is also another technique where you don't use any music or foreground audio at all, you simply play it very quietly at night when you sleep. If it works or not, i leave that to the scientists

There is also the "brainwave frequencies" (see cooledit help) to make your brain "change its status" to that of a more relaxed state, to make you sleep, etc. Usually works by making noise (pink/white/brown) and add a give delay to the second channel. If you listen with headphones its really fun, your brain makes "helicopter/washing machine" noises that don't really exist

Well lossy encoding works with ATH, so i guess it won't preserve much of it... You are better using lossless to preserve such content. I also read somewhere that subliminal messages are not very effective (ie. its effects don't last long) so maybe you could try a different approach. Just remember than visible effects have an invisible cause behind them, so maybe instead of attacking the effect, you could study the cause and find a better solution