as far as I've been told it works like this:
Manga is just a clever word that lets you know that it is most likely a japanese comic - or at least looks like one. Traditionally read from right to left. You know, for fun.
Hentai aparently is derived from a word in japanese similiar to our word for pervert. So you can be a hentai - which you probably are.
"Hentai" just lets you know that the picture you're about to see is going to be a) a drawing of japanese style and b)nude in some fasion.