Hi and welcome to the Reaper *USER* forums.
We arent really a team, just a bunch of regular old users that try and help out when we can.
First off, it sounds like you need to know enough about recording audio to be able to frame your questions better.
First, did you already download the free user manual and/or watch the free tutorial videos here:
http://forum.cockos.com/index.php
It really helps if newbs like yourself can give a rundown of what hardware & software you are using, too.
So: Mac or PC Operating system and version (32 or 64 bit) plus reaper version.
Do you have a proper audio/midi recording interface or are you using the internal soundcard that came with your computer.
Which version of Autotune FX do you have and how are you trying to use it in reaper?
What you should be doing is insert it as an effect in the track effects area - this enables you to use the effect on the track you inserted it on.
Recording the sound with the effect you can leave until you decide you are ready to mix down and render.
Again if you read the Autotune FX manual it lays it all out pretty clearly & if I recall Antares also have a series of tutorial videos for registered users on their website.
Have fun!