Check this link out.
It states that you can adjust your project structure (in your case CSS folders) in project settings.
If I remember correctly you may have to buy it so that you can compile more than 4 or 5 Sass files, but I may be wrong.
Also check that you aren't "only" importing sass partials because of this:
Any Sass and Scss file (i.e. including partials) imported by another file are not shown in the files list but they are still watched by Prepros. The parent file is re-compiled whenever any of the imported files are changed.