That being said, if you're a little creative about how the system works, you can use it for handwritten work. But it's not ideal.
The grading app needs some sort of document to use as the basis for your evaluation. You could just upload a standard evaluation form that lists the assignment's requirement. You'd need a copy of the form uploaded for each individual student.
You then assess the evaluation form as if it were the student's paper while reviewing the physical handwritten work. You can even provide feedback comments and then email or print the marked up forms and return them to each student.
It's a bit of a pain to work this way, but you'll end up with the same data reporting capabilities that you'd get after grading a normal digital paper and will therefore be able to track students' progress--especially if you use Common Core-aligned rubrics (the site automatically calculates progression for all Common Core-aligned assignments; non CCSS assignments are up to you to compare across time).