Editing things using image editors is fraught with difficulty, though I would rather do that effect with layers rather than manually, shadows and blur effects possibly being another.
I have had some success with crystaltile2. It has the option to export and import image formats (do BMP or PNG), and if you are sensible and either restrict the palette (gimp calls it indexed mode) or colour pick when you are there and steer clear or gradients, blur, paintbrush effects (or always use hard edge), anti aliasing and anything else that generates excessive amounts of colours. You might also be able to crush you image down to those colours you do have using such a tool.
It is not always that obvious but for a general workflow open the ROM up, click on the little DS icon to the right of the main toolbar to bring up the list of DS files (hopefully it is just there, preferably not compressed but it can sort that if needs be/you can sort it manually, and not contained in a sub archive it does not understand). Right click on the file you are interested in and it will then give options to load it, do the same for the palette files if you think you want one and hopefully it is not too tile mapped either (though again you might be able to work around that).
From there the image viewer should be there and in all the right modes. Select what you want to edit and in one of the downdown menus should be various export options.
https://www.romhacking.net/utilities/818/
https://gbatemp.net/download/crystaltile2.23649/