It depends upon the exercise. Most of the exercise encourage you to keep the heels down but some of the exercises do bring the heel up.
Here are some links to some exercises that will help:
- Heel Drop Exercise for Calf Pain - https://youtu.be/DJBxefAmexk
- Calf Stretch for Running Injuries - https://youtu.be/PFMYqIP3GOo
Please visit http://exercisesforinjuries.com, make sure to enter your injury or pain in the search box to the right. There is a good chance that I have an article, video or interview that will help you out.