This is simple in XC in RD. I do it by creating a separate team for JV and then do classifications by team. It will score all of them out of one race. So, I have Team A and JV_Team A. You then need coaches to declare if they move an athlete and you need to swap teams for the two affected athletes. So, you need to manipulate the data on the front end to create both teams. What do you use for your entries?
Then under tailor teams, create three divisions ... 1. Varsity; 2. JV and 3. Everybody else in case you forget to move someone to either Varsity or JV.
Under results there is an ignore classification check box that must be unchecked and then you will get by classification results.