You should do your lineart and colouring on seperate layers, not on the background layer. That means when you are done, you merge the sprite lineart and colours (remember to save a file with all the layers so you can easily edit) together and delete (or hide) the background layer. Then when you save as a PNG, the sprite will have a transparent background.
However, if you are using traditional inking methods, you should use this method:
-Scan in your linework
-Use levels to make the lines black.
-Go to the channels and ctrl+click an of the layers.
-Go back to your layers and create a new layer.
-Click on the selection tool, right click and select inverse.
-Get a big, black brush and colour over the linework.
-Now you should be able to hide/delete the original traditional version and your lineart should be replicated on a transparent layer ready to colour. You may need to check for some clean up issues as you will colour in all dark areas.
Overall, I think your sprites are quite nice. I like the heavy linework, but it depends how it goes with your backgrounds. Good luck with it
