(This probably belongs in the
Knytt Stories Level Editing Support board, but I can answer it while it's waiting on a mod to move it.)
I've never used paint.net, though I know lots of other people here swear by it. I use the GIMP, which is free, can do almost everything Photoshop can, and works on PC, Mac
and Linux. (I use the PC version, but I think the instructions below should be the same regardless of OS.)
The gray checkerboard in the image you put up looks like it's meant to indicate transparency; without being familiar with how paint.net works, I can't tell whether it's become part of the image. It might, unfortunately, be necessary to recreate the image entirely if you're going to use GIMP.
In GIMP, start with
File > New..., set it to the size you want, and select transparency for the background.
Now you can either paste in the contents of your paint.net image, using
Edit > Paste as > New layer, or begin recreating the look you want.
If you do have to start from scratch, because the checkerboard
has become part of the image and you
didn't want it there, then I recommend immediately creating a new (
also transparent) layer, via
Layer > New layer... or by pressing Ctrl/Cmd+Shift+N. (There's also a way to create a new layer using the Layers toolbar, which I explain how to open below.) That way, you have a background layer that stays blank, and the top layer (or upper layers) to work on.
To see how the image will look without the checkerboard pattern GIMP uses to show users where the image is transparent, select your bottom layer (which should still be blank), and add a new layer with a white fill instead of transparency. You can either hide this white layer, by clicking on the eye icon next to it in the Layers toolbar; or delete it; or just undo creating it, once you're done looking at how your work will look without the checkerboard backdrop. Just
remember to re-select the upper layer if you're going to make any further edits!
I forget this step all the time.
Once you're satisfied with how it looks, go to your Layers
toolbar -- you can open it from GIMP's
Windows > Dockable Dialogs menu, or by pressing Ctrl/Cmd+L, if it didn't open up automatically when you opened the program -- and adjust the opacity of the layer(s) you want to be translucent. 100% is fully opaque, 0% is invisible, anything in between is translucent.
Now all that's left should be saving your image. GIMP's save function only saves .xcf format, so to get a .png image, you'll need to use
File > Export As.
Hopefully this will get you where you need to be. Feel free to ask if you have any more questions about using GIMP, or anything else related to level-making. And
welcome to the Nifflas forums!