[c-tone]

I agree with Dave above - recording to another track is the easiest way. To make the workflow easier, I copy the entire vocal track to another empty track first, and place Autotune on the new track's insert with no other plugins or automation, then route the output of that track through the main vocal track, duplicate the main playlist (labeling it 'tuned'). That way I can just punch into the main vocal track the parts I want to tune, run on input only to test it out first. The untuned version will always exist on a playlist on the same track this way.

You can also make an Auto-Tune preset with your main settings (such as Graphical, Male Vocal, etc.) and recall that preset. To take it one step further, you could create a blank track with all of these settings including routing on an empty session to use as a template and import that using "Import session data".