If you want a project that fits "portrait" orientation from an iPhone there are a few ways to get this.
-When you create a new project in the project browser on the left side are the presets, if you select Custom from the first pop-up you can enter the proper pixel size for vertical, just flip resolution values. (example: 1080x1920)
-Another option in the project browser is to use the "create project from file" button, this will let you point to a file and create a project that matches it's properties.
-Finally you can edit the project resolution after you create from the project properties (command-J).
For more, have a look at the docs
http://help.apple.com/motion/mac/5.2/#/motn029da09a