overlay two different images (batch)

Ok, the below script will combine files from two different folders then save the result to a third folder. You need to edit the script to point to folders that you have on your HD (lines 2-4). Thre is no error checking, so if you don't have the same number of files in each folder, it will stop and give you an error. If you have any other type of file other than an image file in the folder it will stop and give an error - this included XMP files, so if you're using raw files, change them to dngs first. Right now the script is set to set the top layer to overlay mode. You can change that in line 14.

#target photoshop
var folder1 = new Folder('/c/folder1/');
var folder2 = new Folder('/c/folder2/');
var saveFolder = new Folder('/c/folder3/');
var searchMask = '*.???';
var list1= folder1.getFiles(searchMask);
var list2= folder2.getFiles(searchMask);
var psdOptions = new PhotoshopSaveOptions();
psdOptions.layers = true;
for(var i=0;i<list1.length;i++){
    var doc = open(list1);

    var docName = doc.name;
    placeFile (list2, 100);

    doc.activeLayer.blendMode = BlendMode.OVERLAY;//change overlay mode
    doc.saveAs (new File(saveFolder +'/' + docName.split('.')[0] + '.psd'), psdOptions);
    doc.close(SaveOptions.DONOTSAVECHANGES);
    };

function placeFile(file,scale){
    try{
        var idPlc = charIDToTypeID( "Plc " );
            var desc2 = new ActionDescriptor();
            var idnull = charIDToTypeID( "null" );
            desc2.putPath( idnull, new File( file ) );
            var idFTcs = charIDToTypeID( "FTcs" );
            var idQCSt = charIDToTypeID( "QCSt" );
            var idQcsa = charIDToTypeID( "Qcsa" );
            desc2.putEnumerated( idFTcs, idQCSt, idQcsa );
            var idOfst = charIDToTypeID( "Ofst" );
                var desc3 = new ActionDescriptor();
                var idHrzn = charIDToTypeID( "Hrzn" );
                var idPxl = charIDToTypeID( "#Pxl" );
                desc3.putUnitDouble( idHrzn, idPxl, 0.000000 );
                var idVrtc = charIDToTypeID( "Vrtc" );
                var idPxl = charIDToTypeID( "#Pxl" );
                desc3.putUnitDouble( idVrtc, idPxl, 0.000000 );
            var idOfst = charIDToTypeID( "Ofst" );
            desc2.putObject( idOfst, idOfst, desc3 );
            var idWdth = charIDToTypeID( "Wdth" );
            var idPrc = charIDToTypeID( "#Prc" );
            desc2.putUnitDouble( idWdth, idPrc, scale );
            var idHght = charIDToTypeID( "Hght" );
            var idPrc = charIDToTypeID( "#Prc" );
            desc2.putUnitDouble( idHght, idPrc, scale );
            var idAntA = charIDToTypeID( "AntA" );
            desc2.putBoolean( idAntA, true );
        executeAction( idPlc, desc2, DialogModes.NO );
        
        }
    catch(e){}
    }//end function placeFile

You can do that pretty easily with scripting. Just a matter of defining the two folder, and making sure they are in the order you want. You can then use scriptlistener to get the code for placing a file into another. Then you put all the files from the folder in a new array with the getFiles() statement. then you create a loop to go through that array and open one of the files from one folder, then place a file from the other folder. You can then change the blend mode of the layer to whatever you want, and save and close, or what ever you want to do with the file.