When I started working on my Iphone 6 prototype I drew Iphone screens using the rectangle creator, now that I'm editing in the prototype section to navigate the app, only my first two screens ("iphone 6 - 1 & iphone 6 - 2) worked to navigate to a new screen.
How can I navigate use my self created rectangles to navigate as prototype?
For now you cannot use rectangles for prototyping purposes, you can only use artboards. You can use the artboard tool to create custom size artboards. To solve your issue you could use the rectangles width and height and set them to the custom size artboards. Then use cut/paste capabilities to move other shapes/images you have inside your rectangles. With the newly created artboards you can take full advantage of the prototyping features we currently have.