I will be catching the RER C train from Javel Metro station for Palace of Versailles and returning back the same day. However, on my return leg I need to get off at Champ De Mars which is a little further than Javel. How do I buy my roundtrip? Will it be 2 one-ways from station to station with different prices? Do I have to let the ticket agent know that return station to get off will be Champ De Mars and not Javel? Can I buy my roundtrip a day in advance from Gare Du Nord or any other Metro station or does it have to be from Javel station itself and on the same day?
Within Paris Zone 1 the Billet Origine-Destination / RER ticket to Versailles is the same price between Javel - Versailles and Champ de Mars - Versailles. You shouldn't need to specify that you'll be exiting at a different station than Javel, if you purchased the tickets for Javel Versailles, as long as you're exiting within Paris Zone 1.
You could be extra safe and purchase the RER tickets from Champ de Mars station a day early and use one the next day at Javel to get to Versailles. RER tickets do not expire and can be used at any time in the future after purchase.