If you're looking into putting the sequel to Pokémon: Dark Rising on Generation 4, the latest version of SDSME will actually be able to do such a lot of stuff, it can edit texts, replace map models with ones made with 3ds Max 6 or Maya 7.0. It can also change the music that plays on a map.
I have a tutorial on editing maps in Generation 5, which will help you on editing maps in Generation 4. But instead of using NPRE, you'd use Spiky's DS Map Editor (SDSME) when mapping Generation 4, 'cause it's alot easier. Team Fail's tutorial on editing gen 4 maps will also help you with using the basic functions of SDSME. But even if you choose to keep it on Generation 3, that's OK I understand.
But apart from that, I'm looking forward to playing Beta 2 of Pokémon: Dark Rising when it comes out. It'll be interesting to see what happens in the end of the ROM hack.