Access the waveform view in the options for the autotune plug-in you are using. The waveform displays the pitch of the note as sung by the actual singer versus the corrected version.
Smooth the difference between each waveform so they more closely resemble one another. The more spikes and divergences between each wave, the more noticeable the autotune sound will be on your track. It is OK to "uncorrect" the vocal to some extent because the human ear will likely not pick up a very slight difference in pitch even if it is not perfectly in tune.
Mix the rest of your tracks to more closely match the vocal track. If you are unable to reconcile the autotune sound of your existing vocal track, you can pitch shift the rest of the tracks to more closely resemble the notes your singer has recorded, allowing the autotune to make less corrections.