Well, you can stop synchronization using the settings in the CC app interface and use the web interface to put your files into the cloud or you could put only the files you want to synchronize in the corresponding folder. There is no way to mark a specific file or folder to sync or not to sync.
However, when all files are synchronized (after hours effectively), sync syncs only the new or modified files, which is quite ok.
Regards, Abambo Hard- and Software Engineer and Photographer
I'm not an Adobe employee. All advice constitutes my own opinion. Use at your risk! 🙂