How to customize CoursePress PRO for my site's theme?

I'm trying to get CoursePress PRO setup on my site but the pages are all messed up- tex isn't legible, images are not registering properly and elements of the site and sidebar are all over. I want to be able to reformat them because the are conflicting with my theme somehow.

I also want to be able to remove the sidebar from each post/page within CoursePress PRO. I want to attach screenshots to show the problems but this form doesn't seem to have that option. [attaching them in added comments below]

also, when you are in the course units, it says "there are 0 comments for "course title" but then has pulled a long stream of comments from other posts on my site. Why is this and how do I get rid of them? I don't want any comments on those pages.

How can I correct this all so it's legible and navigable?