Well RGSS and spriting both come with a great deal of practice I can tell you. But you can google for any RGSS tutorials which may help you. As for tiling and pixel art, that is more of a talent you build up through practice, without the aid of tutorials. You can find a bunch of public (but be sure to check) tiles here. That is a collection of tiles I have found on DeviantArt, which has a great resource for them. But to answer your question, yes you may overwrite the tiles in the tileset and simply replace those with new ones. But my advise is to get a tileset like the one you wish you create, using public resources. And use that for your mapping. Reason being is that the current PE tiles are quite outdated and and small. So if you plan on making your game more like the 4th and 5th generations it may be best to simply find a more structured skeleton when it comes to those. Hopefully that makes sense.
