Salt Bridge for Microbial Fuel Cell: Full or Partly Full?
Does the salt bridge connecting the anode (benthic mud) and cathode
  (salt water) have to be full of the agar-salt solution, or can it be
  partly full


There should be no air gaps or cracks so that the circuit does not break anywhere. Take a narrow PVC pipe if your concern is using too much of agar-salt solution.