Both are correct, ie the prayer is that all who have lived in the Body of Christ, will one day have their bodies re-united with their souls, and (Deo Volente) be forever with God in heaven. While the soul goes through the individual or particular judgement, when our souls and bodies are re-united we will go through the General Judgement, where all the secrets of our lives, good and evil will be made known, and (if we go to heaven) we will have glorified bodies, like that of our Lord after His resurrection.