The first step to effective paper-management is designing assignments effectively.
Decide the purpose of the assignment (your objectives for it), make that purpose very clear to your students, and evaluate based on that. Some possible purposes include
When you first assign the writing let students know how you will evaluate it. For example, you may be most concerned that your students understand terminology specific to your field. Organization of ideas is not as important, nor is "surface correctness" (spelling--except of those terms--grammar, etc). In your assignment, make clear your priorities, and stick to them when grading.