It’s kind of strange to hear that GPA points are decreasing. For homework, you first need to open the app on the in-game PC. You’ll get a message on the in-game mail with the program you need to click on.
There are two ways to complete homework: either on your own PC if it’s already fixed, or on the one in the library.
Honestly, I wouldn’t recommend stressing about GPA too much. At the moment, it doesn’t really affect anything except for Milla’s and Isaac’s quests. So once you finish those quests, just forget about it and focus on participating in lessons—that’ll be enough.