By default, S-Docs are saved as attachments in the Notes & Attachments related list on your object record each time you generate a document. To change this setting, all you have to do is open up the template editor for the template(s) you wish to edit, then open up the Document Options tab.
You can configure attachments and files under the Attachment & File Options tab. When Auto Create Salesforce Attachment and link to record is checked (as it is by default), attachments will be created in addition to the S-Doc record for each document that uses that template going forward. If this option is unchecked and used, then re-checked, it will not create attachments for previously created documents. You can also opt to auto-create Salesforce files upon document generation, or auto-create attachments each time a document is edited.
Discussion: There are advantages and disadvantages to using attachments. On one hand, attachments are more permanent, faster to view, and can be exported for archiving or for legal/compliance purposes. Attachments also aren't affected by future template changes, whereas regular S-Docs use the template record each time they are viewed.
On the other hand, the attachment record itself cannot be easily related to multiple records (you should leverage the S-Docs Relationship for this) and attachments can consume a significant amount of file storage space within Salesforce. You also cannot easily report on data located within an attachment. S-Docs lets you choose whether you want to enable attachments or not on a per-template basis. We typically recommend you keep this feature enabled.