Jupiter can automatically calculate cumulative grades, like a cumulative Semester grade based on two Quarters. You do not need to create a separate gradebook to calculate this, because it automatically finds the students' grades from any gradebook, even from other teachers, to calculate the cumulative.
The screen in Admin Mode is where admins define grading periods (like Quarters), final exams (if separate from grading periods), and cumulatives (like Semesters). Also admins may set the options below as defaults on the screen.
The screen in Gradebook Mode is where teachers specify how those cumulatives should be calculated. (Not applicable if no cumulatives are defined, such as four Quarters with no Semesters.) There are three calculation methods:
Unweighted cumulative sum simply adds everything together, e.g. so the Semester is the total of assignments in all three six-week grading periods.
Weighted average, precise lets you specify the weight of each grade, e.g. to set each Quarter to 40% and the final exam to 20% of the Semester grade, or to set each quarter to an equal weight of 1 so the semester is a straight average. (Weights are relative and do not need to total 100.)
Weighted average, by grade is the same as above, except it averages just the grade marks, not the percents, e.g. the average of A- and B is B+. Like a GPA calculation, it doesn't matter if the student has a high A- or low A-, so this calculation method is not as precise. Most schools prefer the precise calculation above.
Show Which Grades
You can select whether students see their cumulative grade or subtotal grade for the current grading period. For example, a student may have 80% for 1st quarter, 90% for 2nd quarter, and 85% for the semester, so you specify whether the student sees the current quarter grade (90%) or current semester grade (85%) when they login. This also applies to what you see on most screens in your gradebook. (You can always look at the screen to see all grading periods together.) System admins may set the default for this on the screen.
If weights for one class keep saving for other courses/subjects too, uncheck "Apply to all classes/subjects". But different sections of the same course/subject must have the same settings.