Photocraft has been working alright for me. I really struggled to learn GIMP, and I haven't found any easy lightweight image editing tool that replaces Paint.NET for me before trying Photocraft. It's still a little confusing since I'm not used to photoshop-like bindings and layout, but it hasn't been too hard to adjust. (I also only ever use it for small simple edits, drawing, cropping, color gradients, background removal, etc.)
I easily modified pinta to do exactly this. You mean overlay, right? It can overlay, draw, manipulate, and I added a better file navigator so I can see which imagery I want to overlay to begin with. My use case was scientific in nature. What is yours, if you don’t mind my asking?