Hi @magichristopher, the exported files from Webflow use relative paths, so you just have to adjust paths in your exported files for links, images etc, to point to the correct files on your site.
For example, if I have a default path of:
and my images are really located on my server in subfolder-two, then after export, I would change my image path to be:
If my image was in subfolder-two and then in another subfolder after that, such as subfolder-three, then your path would be:
Since you are the one who is making the structure in your external site, you just need to plan out how you will store your css, images, scripts etc, and update the paths to those in the html exported file. You may also need to change your css files to change the path of any background images used in your designs to point to the correct path locations.
I hope that helps, cheers.