Next time, I'd really advise you to create two separate courses, one for each subject. However, what's been done has been done.
Here's my question: Are you simply hoping to calculate your students' grade percentages and then you're entering the letter grades in a separate system such as SIS? That's how grading is handled at my community college. If this is the case, then I can suggest a solution for you.
First, put all of the students' graded work into Assignment Groups. You might end up with something like this:
- Math Weekly Quizzes
- Math Homework
- Math Chapter Exams
- Math Final Exam
- Science Weekly Quizzes
- Science Homework
- Science Chapter Exams
- Science Final Exam
To calculate the grades for Math, use percentages such as these:
- Math Weekly Quizzes 25%
- Math Homework 25%
- Math Chapter Exams 25%
- Math Final Exam 25%
- Science Weekly Quizzes 0%
- Science Homework 0%
- Science Chapter Exams 0%
- Science Final Exam 0%
Then reverse the percentages for Science.
I would strongly advise you to go into your Course Settings, click on the tiny blue letters more options at the bottom of the page, and "disable" the students' current grade percentages. It will be too confusing for your students to see what you're doing behind the scenes to calculate their final grades.