Ah, the joys of breaking in tall boots.... Yes, it will hurt. :) You will most likely get blisters and your legs will slide around when you ride. But it will be worth it in the end! (as long as you don't grow out of them too soon! wouldn't that be horrible?). Put lots of conditioner on the ankles and the INSIDE only of the boots and wear them as much as you can. I also work the leather a little around the ankles (gently roll it between my fingers) At night fold them at the ankles (as if your heel was going way down) and put them under your bed or a coffee table or something so it stays that way over night. When you ride use something like Saddle-Tite (or my favorite, something German called.... Halfty Haft?) to keep your leg from sliding so much. It should take a good week or two of daily riding/walking to be comfortable.
I know a lot of people showing in Beginner who just wear nice half chaps with paddock boots and do well. But, if it ever comes down to you and another person in an equitation class the judge will pick the more appropriately turned out of the two.