To test, I created a new SSIS project named “DeploymentTest1” and added three simple SSIS packages. I right-clicked Package3.dtsx and clicked Deploy Package. The Integration Services Deployment Wizard started, as expected. Since I was deploying to a pristine Catalog, I created a new Catalog Folder named “Deployment”. There were no projects in my catalog, and I was curious how the Deployment Wizard would handle this.
Andy notes that this works, but you might want to stick to the tried-and-true method of deploying entire projects and naming your catalog project the same as your SSDT project.