Just replace toggles.bat in the folder with this version. These are the recommended settings for using the practice hack:

Cutscenes removed: End Of Day, Area Unlock, and Pikmin Discovery. RNG changed: Snagret 90%, Nectar 20%, tripping 1/3rd as likely.

This is what I believe is optimal to practice with. If you want to change your own toggles.bat file, you can do that too.