More likely to be "me and you together", meaning I want to be with you even in my dreams. "me in you" would mean sexual intercourse, and the "together" would be superfluous.

"I will have a dream with me 'n you together" still sounds awkward. "I will dream of you and me together" would be more natural "I have a dream of you and me being together" would also work although it has a different meaning

Sometimes, in spoken English, "and" gets reduced to an "n" sound: "me 'n you". This is probably what you heard.