Take a look at [320andup scss-compass files](https://github.com/malarkey/320andup/tree/master/scss-compass).
See how “320andup-scss-compass.scss” file imports all the stylesheets into one file.
This way you can organize your code.
If you need to move CSS code into SCSS just simply create new file “mycoolfile.scss” and copy the CSS as is, or rewrite it so that is represented in SCSS format. Then just compile the file.
>I assume it’s because compass thinks that all my css and scss files should be in a single folder rather than in bits and pieces throughout the site.
You should keep all of your files in appropriate folders. If you try to modify some code 6 months from now, will you remember where the file is located? If you develop solid structure to the way you organize files; will only make your coding experience easier.