I've been out of the game for a while so a lot of old problems are creeping up again.
The one right now is that I am saving .png on Paint.Net and after getting the dithering levels to 0 and setting the saves to 8-bit depths I'm managing to get the files imported into the software, but it's seeing black as the "transpoarent colour". I read that when you save a file, it reads the first colour in the palette as the transparent colour which is why black would be chosen. I went into the palette save folder and changed the colour from FF00000 to the code for the same green background that the RTP has and resaved the images, but upon import it was yet again viewing black as the transparent colour, and by now all the RTP is coming up as such as well and I've no idea how to even get the original files back to normal much less save new files for that. I had to just delete all the broken files and replace them with the original RTP.
Kind of annoying though, because if I can't seem to get a file saved in a way that RM can read it then I'll never be able to use any other images