Blisters are going to form from some improper gait mechanics. Your gait can be imbalanced from any stress - running shoes, old injuries, dietary stress, training too hard, etc. So muscle imbalances occur and blisters form. Ideally you need to let them heal up which may mean bandaging them up a bit.
Changing up your stride can also help-blisters should not be an ongoing problem. Check into shoes, stride, training schedule or other issues that are potential contributors to the problem.