Paint.net had a lot of promise for a nice lightweight free image editing software with some big-boy features but they stopped just short of actually achieving it by leaving out key features that just are absolutely 100% needed to properly work with layers.. You ran into one of those..
Either buy Photoshop or download the Gimp/Gimpshop (Google both). You're going to hate it (Gimp) at first, you will be completely overwhelmed but stick with learning it.. All the powerful tools you need are there. It's the closest you'll get to Photoshop without having it. It's just from a design and layout standpoint the developers of the Gimp succeeded in making one of the worst user interfaces I've ever seen.. But it's free and great.. Just a huge learning curve..
