It’s probably simpler if you put the actual client folders in EagleFiler. That way you don’t have to worry about keeping EagleFiler up-to-date or about duplicate files.
If your folders were all local or all on Dropbox, you could simply create an EagleFiler library that location and then move the existing client folders into EagleFiler’s folder.
But it sounds like you want parts of the same library to be stored in different places. In this case, you should create the library in a non-Dropbox folder and move the existing local folders. Then you would add one more symlinks for the client folders that are on Dropbox. There’s some discussion of this here and here, and I can help you more specifically if you provide more information. For example, are all of the Dropbox client folders within the same subfolder? If so, you could just link that from EagleFiler. Otherwise, you might need one symlink for each client folder.