Yes, "Notes" and "To do Notes" are different systems, even though you can launch a To Do Note from an existing Note to a Customer or Supplier.
To Do Notes are accessed from Company > To Do List, and are used for company file wide tasks.
You can create only one Note on a Customer or Supplier. If you want more Notes for the same Customer or Supplier, just add it to the existing Note. In the Customer/Supplier Centre, you can adjust the table of transactions downwards to show more lines for Notes.