One thing that Creator is not good at doing is versioning. You have to do it all manually.
What I do is create a folder to contain my project. The folder name is something like "My Project - A.2" where A.2 is the version number. Under this folder put all creator projects that are part of the solution. In my case, I have a Bootloader and Bootloadable as two separate projects that are in this folder. They are named something like "My Project - A.2.cydsn" (this is the bootloadable) and "My Project Bootloader.cydsn". In this case the bootloader does not have a version number as it should not change through the life of the product. But it is still important to keep it together with the bootloadable.
To start a new version, make a copy of the entire structure and only rename the root folder (My Project - A.3). Then open the projects under this folder and rename them using Creator. I usually rename the projects first and then the workspace (I have a workspace stored in the bootloadable project that opens both the bootloadable and bootloader). Allow Creator to rename ALL files in the project.
Hope this helps,