What should I do if there is an assigned story or chapter that I am uncomfortable reading?

The decision is up to you. You are the teacher, and if you want to skip something, it is your choice. But don't take this responsibility lightly! Consider how this book (or chapter) could be valuable and enriching if taught carefully. Then weigh the pros and cons. Perhaps take some time to read I Can't Believe You Use That Book! 

If you still feel strongly about skipping, then feel free to do so. Sonlight provides plenty of resources for your school year.

Remember: These programs are guides and helps, not taskmasters.