The lady at the boot store told me to wet the boots with a mixture of rubbing alchol ands water, then take a golf ball, or back of the spoon, and push gentle outward where it needs to be fixed.
Wow! I am having the same exact problem...I just started to ride in my boots and I have two big blisters on the backs of my heels (lol) but the leather tall boots with zippers do eventually form to your calf and foot and they have dropped about a half an inch already! Yay!
A tip for tall boots that might be helpful is you can use heel riesers until they drop some. Also they make gel bands to help protect from rubing that causes blisters. I used both for my tall boots and they worked wonders. You can find them at your local tack stores usually.