Ratchethead seems to answer my question pretty well, my brother is the one with sonar on his computer so I haven't had a chance to play with Ratchethead's suggestions yet, but it seems to be what I am looking for.
To clarify what I had said in the beginning, basically I have a VST plug-in, that occasionally I only want to affect certain parts of a vocal take instead of the whole vocal take. Using auto-tune was a bad example for my case, but maybe I gave the wrong scenario.
Lets say for example I had recorded a rapper rapping a verse, then a singer singing the chorus right after him on the same vocal take. (Im not that sloppy w/recording techniques but this is purely for example.) Now lets pretend the take was perfect and instead of having them re-record and etc, I wanted to just apply auto-tune or some kinda effect like a delay or what not to JUST the singer singing on the chorus in the take. Instead of applying the delay, auto-tune or whatever else I want specifically highlighted to the whole vocal take.
I hope this clarifies what I am looking for. I avidly recorded on nothing but mediocore daws before, so I am having a lot of manipulation problems with sonar.
Oh btw, if anyone checking this thread knows how to do the pitch shift through sonar to do the downsouth "screwed" effect on vocals, that info would be handy as well. Which is applicable to why I need better plug-in manipulation.
Edit: Yes Ratchethead's method works fine. Thank you Ratchethead, I've been at this for weeks and its been driving me insane (btw I hate that it was so simple in the end) THANKS!