Both are Hebrew words. Amen comes from the Hebrew word "Emunah" (which means faith). Saying "Amen" means I believe (or have faith) in what you just said (or prey), Halleluyah is a word combined of 2 words: "Halelu" is plural of "Praise" and "Yah" in Hebrew is one of the names of G-d. All together is Priase G-d (in plural.... so not referring to one man but to the congregation).