If you have been awarded time as a result of submitting a proposal, the Phase-1 Science Goals will be automatically copied over to the Program tab of the Project Tree and the project will open here when retrieved from the ALMA archive (see Section 7.4). Technically speaking, the Science Goals that are shown in this tab are Phase-2 Science Goals, but their visible content is absolutely identical to that of their Phase-1 counterparts. If a Phase-2 Science Goal is instead being created from scratch, these are instead created in the same way as described in Section 5.3 for the Phase-1 variety. A Phase-2 Science Goal is most-easily created by clicking the icon in the Toolbar, but right-clicking on the Science Plan folder or opening the Edit menu will also work.
It is worth noting that, for those people with the necessary privileges, it is possible to copy a Phase-1 Science Goal (e.g. with Ctrl-C), to open a new Phase-2 Program (from the File menu) and then to paste the copied Science Goal into this.