i can't seem to get it to work. I've copied the battle engine folder into my repository but when I compile it, it creates normal emerald without the changes. Can someone help?
What exactly do you mean by that?
Normally, if you're not using Git, one way to go about compiling the battle engine v2 would be to download the battle_engine_v2 branch as a ZIP from the GitHub Repository's website, install pokeruby-tools on it like you normally would, and then compile.