You can add new sequences to an alignment using the Add submenu in the Actions main menu or the context menu.
There are two ways to add a new sequence to the current alignment:
From a file in the compatible format (FASTA, GenBank etc.). The list of the supported data formats can be found here.
From the current project.
If you activate this item, the following dialog will appear:
You will see the Project View tree filtered to show only appropriate sequences. Select the items to add and press the Ok button.