How can I compare two different sets of students assessment marks, when they are all in the same class?

Go to; "My Subjects" and click on your class. 

Click on "Class groups."

Here you can create two class groups - in the drop down next to each child, select if they should be in Group 1 or Group 2 ( you can select up to 10 class groups.) 

Now, when you run the Markbook you will see "All Students" click on the drop down list to choose 1 or 2 and click "Choose." 

Note: You will have to select one group at a time to view the data.