WorldPainter is a great tool, can make new terrain or edit existing worlds. (Through importing). You can flag the world to populate when you're exporting, so Minecraft will go through and add resources on first play-through. I haven't tried this with Tekkit yet, but it sounds pretty promising from my past experience with it.
http://www.worldpainter.net/
Adding a thought: You can paint your biome layers any size you want, so you could use this for larger Biomes.