The proposition contains two parts. Part 1: Evil was rooted only in... This explains where the root of evil lay. Part 2: Therefore, in order to complete them... This explains what these vessels had to contain in order to carry out their function.
Part 1: Evil was rooted... For Atzilut itself consists of nothing but the laws and measures of the divine Mind (המחשבה, hamachshavah), these being the Sefirot. However, the production of the branches (i.e. the separate creatures) depends on Beriyah, Yetzirah and Asiyah. As explained earlier (in Opening 39, Part 2) there are two roots. The first is a root that produces branches of the same kind as the root itself (i.e. the branches of Atzilut itself, which are all on the level of Godliness). The second is a root that produces branches that are not of the same kind as the root itself – i.e. the separate creatures. (This second root is the power of Tzur Tak, which brings forth its “branches” in the form of the separate creatures in each world in accordance with the root of that world in Atzilut. The roots of Beriyah, Yetzirah and Asiyah in Atzilut are respectively Imma, Zeir Anpin and Nukva of Atzilut.) Since there are two roots, Beriyah, Yetzirah and Asiyah must in each case first come forth on the level of its root in Atzilut, and only afterwards, through the second root, the power of Tzur Tak, as a realm of separate creations. We may thus infer that actual evil itself exists only in the branches of Beriyah, Yetzirah and Asiyah – the separate creations – and not in the branches of Atzilut, which are on the level Godliness itself, where evil is not applicable.