mixmkr
All female harmonies are Melodyne generated.  
https://www.youtube.com/watch?v=6gJXOAEVFPA

May I assume the basic vocal was sung by a female voice?  The harmony is also  fairly close.  Again ... my problem probably lies in my expecting too much as my bass vocal is brought up to a  soprano's  range.  It just ain;t gonna happen unless that soprano happens to sound like a chipmunk!    

Anderton
Oh, and one more thing...humans don't gravitate to even-tempered pitch but to just intonation. If you don't believe me, run an analysis on string ensembles and barbershop quartets, neither of which is constrained to even-tempered tuning. Often after creating a quantized harmony, I'll open it, turn off pitch grid, and make some slight adjustments to create what "sounds" right. 

I'm not terribly familiar with  what you are suggesting but I have found myself un-checking the Pitch Grid Chromatic Snap and making manual pitch adjustments.  

mettelus
+1 to the above. Melodyne works best when given clean (no effects whatsoever) audio data, and asked to process that data by small amounts. That said, it is much more effective to (sparingly) correct random misses on a harmony that was sung, rather than shifting a melody 4-5 semitones to "create" a harmony from a melody line.

By the way besides attempting way too much range adjustment I have often committed the no-no by using  Melodyne on top of Reverb and other FX.  In fact that might be  the more critical error.  

Craig's advice is on the money with attack and intonation. There are a lot of interesting tricks that can be played to keep focus on the melody (where it should remain) and the harmonies be supportive.
 
I honestly have not stress-tested this in great detail yet, but I do have a keen interest in this topic, as I have projects I want to give full choruses to similar to how done by Queen and Def Leppard... but the method used by them was actually recording the same phrase multiple times (in many cases over 200). The "Let him go" that hangs in Bohemian Rhapsody is actually Roger Taylor's falsetto (not pitch-shifted... that is truly him).
 
If you are open to such, post an unprocessed melody line (doesn't need to be long), and shoot me a PM on what you are looking for with the harmony and link to the file. This is something I would like to understand in better detail as well.

Always clean... Celemony actually has a good tutorial video on why (http://helpcenter.celemony.com/essential2/en/singletrack_tutorial_guitarsetup.html). But even with this said, SONAR will process the Region FX prior to the FX bin (http://www.cakewalk.com/Documentation?product=SONAR%20X3&language=3&help=Mixing.07.html). Where this can cause grief is if you render those effects into the clip itself (such as bouncing to a new track).

mettelus
If you are open to such, post an unprocessed melody line (doesn't need to be long), and shoot me a PM on what you are looking for with the harmony and link to the file. This is something I would like to understand in better detail as well.

I can probably figure out how to PM you or find an email address! I'l try and send you something tomorrow.    It'll part of an challenge to fix the awful True Love  tune I posted in the style of Elton John and Kiki Dee.  There is a part  I'll try to do (without FX etc) where each vocalist belts out  some blusey type stuff ...  in falsetto most likely.  I tried electronically  up'ping my voice and ocatve to get it to sound good but it (among many other less than good things in the piece I did)  it came out poorly.   I'll also send the version by Elton and Kiki  so you get the feeling as to what I would like to accomplish!    
 
By the way  several years ago I heard Bohemian Rhapsody done acapella live at the King Center in Melbourne Florida by the Ten Tenors of Australia.  I always thought the piece was extremely  intricate and very well composed but until it was introduced by the Ten Tenors I didn't know Queen  from white whale manure.  It is now one of my favorite pieces.