Two ways. Both require some manual steps.
Make the document as one, and then make a copy - remove field codes and separate them into the documents you need. (this way will ensure any citations used in the text and the table only apear once).
2nd way is to create the two documents, and then using the edit bibliography, to change the "number you start with thru the bibliography menu in Endnote. See attached image. – but then you will still need to copy the bibliography to join the two, and if the citations is used in both the text and table, it will apear twice.