I'd highly recommend using SDSME to edit trainers and scripts instead of PPRE, and using a separate ROM to edit wild Pokemon (once you've finished editing, just copy the narc with the wild data to your actual ROM; this way PPRE can break whatever it wants and it won't affect your actual ROM). Don't use SDSME to edit wild Pokemon because it doesn't seem to work properly on any map with water.
Have you got any scripting experience with the GBA games? If not, that's actually a good place to start. There aren't many resources around for the DS games, but their scripts are very similar to the GBA ones, so you should be able to pick up the basics from something like
this tutorial. Not all of it will actually be useful (for example, you don't need to worry about pointers, and some of the functions will be slightly different). The best way to learn how to script something is to look at how Gamefreak did it, and just copy and modify the parts of their scripts that you need to make yours. With a bit of practice you'll eventually be able to write them from scratch.