Is there a way to upload documents only related to SOAP notes? I do not want to mix it with patient documents

Yes, you can upload documents that are related to SOAP notes in "Patient SOAP Documents" under the Related Tasks section in Patient dashboard:

By clicking on the Add button users can add SOAP Documents as required. They can enter the document title and it's descriptions:

Once the users select the required file from the mentioned file formats he/she should click on the Upload button:

Once the document is added the users can view, edit or delete the document if required.

Note: Only the mentioned file formats will be accepted while uploading the files.