Hi Florian
That's exactly how I've been using BoxCryptor for about 18 months now, until I needed to reinstall.
All I need to be able to do, is to remove the Dropbox location which is setup by default by BoxCryptor, so that I can then add the subfolder which I've always previously used for BoxCryptor. Is there any reason why the remove button for the Dropbox location is greyed out, so that I can't remove it?