why do acidify the aqueous layer

Answer 1

Your question is a bit vague, but I will try to answer it.

If you are referring to adding an acid to a reaction flask, then you are likely trying to complete an acid-base reaction that will protonate (neutralize) a base. This will result in any charged bases in solution becoming neutralized. Neutralized bases will move from the aqueous layer (where charged molecules are soluble) into the organic layer (where non-charged molecules are soluble).