I would get the new insoles first. Then heat mold them with the insoles in the boots.
When I heat mold my boots, I make sure and wear the socks that I ride in. Some places will advise against this apparently, but I think it makes the most sense.
When the mold them, they will heat them up, (takes about 10-15 minutes), have you put them on and lace them up tight, then they have you stand with your toes on something, sometimes a 2x4 or something similar for about 15-20 minutes. Then you are done.
Extremo is right, you will probably hate the superfeet at first. They aren't designed to be squishy comfy. They are designed to provide support. I bought a few pairs so that I could outfit my shoes with them as well. Now I am hooked. At first though, the transition was difficult, My feet were a little sore for about 2 weeks.
let's not talk about it