If you can't do that you'll also run into like a million problems later and nobody will want to help you solve all of them. Learn the program first and then make the game. Watch a tutorial.
In paint.net when you're exporting your png set it to 8-bit
Stop using RPG Maker 2000 or some shit, upgrade to MV or VX Ace.
If you're making a game in RPG Maker 2000 or 2003, get Aseprite and make 256-colour images in it. (It has a free beta on the official site.)