I've done this, so here is what you need to do:

1. go to United.com and find the flights you want and confirm R seats are there if you want to do the upgrade without waitlisting after ticketing. Price out the ticket, note the fare class of each segment and the fare basis

2. call Chase UR travel department - tell them you want them to book specific flights in a specific fare class. If you get a decent agent, they will do this for you, if you get a lazy one, escalate to a supervisor - you may need to hang up and call back multiple times and may need to spoon feed them each flight, booking class, and possibly the fare basis they need to ticket in each direction.

3. once the Chase ticket is issued, go back to the reservation on united.com, where it should show up if the FF number was attached , then select the Upgrade Reservation link and follow the normal process