For Fates hacking specifically, there are a few places that you can look at to get started.
- RainThunder's repository/wiki. At the least, I suggest reading the BIN file page in case you need to do any hex editing. You can also find a list of important files at the bottom of the BIN page. The other pages on the wiki can help you figure out where things are located in the ROM. I'd also check out the repository - RainThunder has a lot of useful tools there that you'll definitely want if you decide to do any Fates hacking.
- You can find a couple of my own tools here. The script editor and person editor would be useful for making changes to levels.
- FE14 Dispos Tools can help you edit map spawns.
- In general, the Fates ROM hacking general thread is the best place to go if you need help. The main post has plenty of notes about file formats as well as links to useful tools. If you don't know how to do something, you can get help pretty quickly by asking in that thread.
Thanks a bunch, and one last question: To start as a base for these edits, is there anyway I can find the vanilla fates gamefiles to edit or would I need to use my own copy?