When あなた make 愛 あなた involve feelings, LOVE, passion. When あなた have sex あなた just have sex, without 表示中 your feelings for the person, with no affection, with no sweet words または whatever, that's just sex.
Well both are pretty much the same. Making 愛 can be also be キス and caressing other than intercourse and it also can be others like oral sex and anal sex (especially for レズビアン and homosexuals).