You would add it to the original line, but keep it inside that first bracket. Look at this example here:
Syntax: layerQueries={ Layer_or_tableID1 : {"where":"attribute query" , "useGeometry" : true | false, "includeRelated" : true | false}, Layer_or_tableID2: {.}}
Create Replica—ArcGIS REST API: Services Directory | ArcGIS for Developers
So if I took the first example you posted in this thread and corrected it, it would look something like this:
{"0":{"where":"Project_Number='842'"}, "1":{"where":"Project_Number='842'"}, "2":{"where":"Project_Number='842'"}, "3":{"where":"Project_Number='842'"}}