I encountered the same challenges changing seating assignments yesterday. This is, unfortunately, the best way I've figured out how, even with a TrueBlue-linked reservation:

1. In the top right corner of the jetblue.com homepage, click "HELP."
2. Click "MANAGE YOUR FLIGHTS," the second heading.
3. Click "CHANGE SEATS" near the bottom of the list.
4. Click the "ONLINE SEAT CHANGES" link in the paragraph entitled "CHANGE YOUR SEAT ASSIGNMENT."
5. Enter your info, click "CHANGE YOUR SEAT," and change your seats!

As onerous as this process sounds, it's an improvement over a few months ago, when you had to go through this scary reconfirmation process when changing a seat that resembled the same process you go through to change or cancel a reservation, and made it look as though you might have to pay a change fee in order to revise your seating assignment (you didn't, but it was kinda scary nonetheless).

C'mon, JetBlue. I know you can do better.