It's true that you need a good GPA to get into a good college, as well as good SAT scores and a number of other things. It would be a good idea to identify the school you want to attend next year and talk to them right now to find out how they're going to count the grades from your current school. It's possible that they won't give you credit for any class that isn't part of a standard high school curriculum, which means that the grades for the non-standard classes won't count and it won't matter how well you do in them.

If the new high school DOES consider the grades from these classes, then obviously it's better to have a higher grade than a lower grade. But you can always tell your future college the story of how that was an exceptionally difficult year, but you worked through it and learned about things like setting priorities and solving real-world problems. This is character-building stuff and colleges like students who can overcome difficulties. Plus you'll be able to show them that you improved your grades, assuming that you do well during the rest of high school. That counts for a lot and if you have to blow one year of high school it's much better to blow your freshman year than your senior year.

It's wonderful that you and your mom are having discussions now on subjects like planning for college and how high school relates to it. It sounds like you're starting to work together and are moving toward cooperation and a meeting of the minds, which is much better for both of you than what was happening before.