oneworld - Merging a Reward Ticket with a Paid Ticket

I've been steadily accumulating BA miles for 3 years now and have booked a ticket from JFK to Sydney in business class. However I live in Halifax and need to get to JFK first. I thought of booking the whole trip together, but with American Airlines YHZ-JFK and then Qantas JFK-SYD it would of taken around as many points to fly in Y as the J Ticket I booked. So I'm going to buy the American Airlines flight myself.

Now my question is once I have the paid American Airlines Ticket and the Reward Qantas ticket can they be "merged" together? If so what is the process.

I don't understand what you mean by "merge", although the answer is probably no. What are you hoping to achieve by whatever it is?

Just ring QF and say what your arriving AA flight is - so they know where you "might" be if your incoming flight is late. They should put a remark in your QF booking. Of course, if on different tickets, QF may not have any obligation to wait if you are delayed. Give yourself plenty of time for the connection.