you could have the TA book for you, so that you could use the travel cert. They will do the same as you, go on line and click a few links then apply payment. You need to ask if the TA will do this for you, as they will have to make payment on your behalf to jetblue.
They will not be able to directly use the travel cert with jetblue, they will book the flight and then add it to your bill with the TA, and then use your travel cert to cover that. As yor TA has all your information, they can book for you using a just let them know what seats you would like and all should be fine.
Penny
Remember JB has extra leg room in the back 2/3 of the plane.