We've setup a test integration with Zoho CRM. On the "Save Quote As" popup, is it possible to have the "Create new Linked Document" and "Create or Attach to Deal" checkboxes be unchecked by default. This would be to prevent the user from accidentally creating a new Deal, etc. (see attached screenshot)
The checkboxes are remembered (per user).
The be able to uncheck the linked document go Tools > Options > Synchronization and uncheck the box, that usually does the trick.