You only need to download arduino and teensyduino once. I think you only need teensyduino also.
The .ino file will need to be in a folder by itself, with that folder being the exact name as the .ino. You can put that folder anywhere. If you make multiple copies for different projects, you need them in their own respective folders.
If your code is giving errors, it is most likely that you deleted a comma or bracket somewhere while mass editing. I recommend keeping a clean copy of the code somewhere and working on a new saved file. Remember you can copy mass portions that you know are good, and paste them into new clean project file.
If the board isn’t uploading the code correctly, make sure the settings under TOOLS are correct. (midi/keyboard)