Leaving the mouse pointer over any section of the diagram should bring in more detail.
Note the path of electrons shown above in red and protons (H+) in blue.
More electrons and protons pass in from reduced NAD than from reduced FAD because more reduced NAD molecules than reduced FAD molecules are produced in glycolysis and the Krebs cycle, and also reduced FAD misses the first stage (involving Complex I) so fewer protons are pumped and eventually less ATP is generated.
The final action is the production of ATP by addition of an inorganic phosphate (Pi) to ADP. Since oxygen is involved this is called oxidative phosphorylation.