I know that this is my first post here, but I have been using Paint.NET for a while and would also like to thank all that are involved in the project for creating such an easy to use, free application.
I agree with the author of this thread in that it is extremely useful and will remain on my computer for a long time.
As to the question posed by the originator, I might be missing your point entirely, but can't you just use the blue arrow in the top right of the toolbox to move the layer (assuming your background is transparent)?