Welcome to the zenAud.io community site
Take a look at this tutorial on Scripted Control Automation:
In this way you can pre-program parameter changes of your plugins at certain points in the song. If your autotune plugin has this parameter then you can certainly pre-program the change.
As for your question on imported audio, we will be adding our own audio editor (as well as a MIDI editor) in the future. For now its advised to edit in another application. For quick edits, I can recommend Ocen Audio, its a free audio editor: https://www.ocenaudio.com/