Measure the amplicon concentrations, for instance on the Agilent Fragment Analyzer, using the NF-910 dsDNA Reagent Kit for 35-1500 bp fragments (according to manufacturer's protocols), followed by a smear analysis using the PROSize 3.0 software on the range between 350 bp to 550 bp.
Using the measured concentrations, now pool each plate of samples equimolarly into a 1.5 mL lowbind eppendorf tube, either manually or using a liquid handling station such as the Qiagen QIAgility or Opentrons OT-2.
Depending on the accuracy of the platform, it is advisable to make sure the lowest and highest concentrations do not differ by more than a factor five. Either (1) pool low and high concentrations first separately, (2) first dilute samples with very high concentration, or (3) process any samples with very low concentrations as if their concentration is 1/5th of the highest concentration. Also include controls (blanks) in the pool.