Thanks Jim for your helpful response and I can fill in a bit of clarification. Unlike in the D3 in which slot 2 is the only assignable with three mode choices, in both the DR4 and D800E the user selects the Primary card and then how the Secondary card (slot) is used. Your understanding appears correct substituting Primary for slot 1. The NEF file will always be written to the Primary slot and then there are three choices for the Secondary slot (viz Overflow, Backup, or NEF in Primary + JPEG in Secondary).
It would seem a JPEG file to either card would be a separate file (picture control or customized setting selections vs NEF data). So does the NEF file writing have to complete before the in –camera processor starts the JPEG file sending or does the in-camera processor recognize two independent files and sends the data to the respective cards as specified by the user simultaneously at their own write request speeds. (When two chips are present, I believe the camera does not know the speeds of the chip and that the chip controls the receiving data rate.)
This simultaneous vs sequential file handling aspect of the camera’s processor would seem to determine the optimum selections for fastest clearing of the buffer when more than just NEF files are desired.