Is there a specific file I need to program them into or just put them into their original file? I don't want to mess up whatever setup you are trying for.
You can use the Extend Thing mechanic to add core spells to a class spell list. Take a look at the Complete Adventurer for an example. Do this in the file that contains the class.
For non-core spells, you can modify the spell directly in whatever file it is contained in. Just make sure to add any necessary sources.