In full scale you need to add EM to one of the faculatative ponds and keep the other one work without EM and take samples from the outlet both ponds , so you can assess the performance of useing EM with this pond, I think this is the best way to do that in full scale , or you can made a lab scale ponds and work in the lab 

Determination  of waste biodegradation before  after introduction of  effective microorganism 

I think you don't need full scale experiment. You can do this in laboratory scale. For example, add EM to one of the 5 L reactor and keep the other one without EM and go on as Mr. Alabdraba stated. However you need adequate illumination for support algal activity.

I think you also need to include as many replicates in your experimental treatments as possible.  There tends to be quite a lot of variability in the use of EM.  Also, each replicate should be kept as isolated from the others as possible.  Many bacteria can exist viably on just the mist above an aerated tank or other water body.  The risk for cross-contamination and therefore an irrelevant experiment is high.  Starting with a relatively small experiment is a good idea before spending the time and effort on a large scale demonstration. 

thanks for the replies! For replicating the Facultative lagoons, should I use the same water depth of the full-scale lagoons (2 meters) and the same detention time? Consider the microorganisms are added to the lagoons as a slug, not on a continous basis

The best estimate would be to analyse the COD level at both entry and exit ports and work out the relative efficiency (difference/intake %) of the organism to lower the COD at the feeding end. As you mentioned it is difficult to reproduce faithfully at a pilot scale the conditions that prevail at field scale treatment plant.

My thinking is that you can analyze the BOD levels as well, I mean in addition to the COD levels