Ok, my problem....merging two unique files batch Process

Ok, my problem....I have been deconstructing films, so I have thousands of picture files for batch processing in Photoshop (Resizing etc) What I would like to do is batch merge two or maybe three lots of deconstructed film footage image files from different sources, one as a background film image file and one as the forground film image file layer, thousands of images all at once, after they have been processed first in photoshop, so I have seperate folders with the image files in each folder, they need to be combined in sequence as I want the image/frame numbers to match up in each folder, then combined to non merged layers and saved into another folder, I want non merged layers, so I can use an action later to balance the overlay. I know premiere and After Effects could maybe do this, but I am looking for a different kind of effect.....thanks 

This might help, but very probably one of the more experienced Scripters has a Script (possibly with a more comfortable interface or more features) for that, too:
#target photoshop
// dialog for folder-selection;
var theFolderOne = Folder.selectDialog ("select a folder containing the backgoround images");
var theFolderTwo = Folder.selectDialog ("select a folder containing the foreground images");
var theFolderThree = Folder.selectDialog ("select a folder to save the combined images to");
if (theFolderOne && theFolderTwo && theFolderThree) {
var theFilesOne = theFolderOne.getFiles(checkFor);
var theFilesTwo = theFolderTwo.getFiles(checkFor);
// check if both folders contain the same number of files;
if (theFilesOne.length != theFilesTwo.length) {
alert ("the folders don’t contain the same number of images")
// else do the stuff;
else {
// create the psd-options;
psdOpts = new PhotoshopSaveOptions();
psdOpts.embedColorProfile = true;
psdOpts.alphaChannels = false;
psdOpts.layers = true;
psdOpts.spotColors = true;
// run through the files;
for (var a  = 0; a < theFilesOne.length; a++) {
// open background-image;
var theFile = app.open(File(theFilesOne[a]));
theFile.activeLayer = theFile.layers[0];
// place foreground-image;
var idPlc = charIDToTypeID( "Plc " );
var desc6 = new ActionDescriptor();
var idAs = charIDToTypeID( "As  " );
var desc7 = new ActionDescriptor();
var idfsel = charIDToTypeID( "fsel" );
var idpdfSelection = stringIDToTypeID( "pdfSelection" );
var idpage = stringIDToTypeID( "page" );
desc7.putEnumerated( idfsel, idpdfSelection, idpage );
var idPgNm = charIDToTypeID( "PgNm" );
desc7.putInteger( idPgNm, 1 );
var idCrop = charIDToTypeID( "Crop" );
var idcropTo = stringIDToTypeID( "cropTo" );
var idboundingBox = stringIDToTypeID( "boundingBox" );
desc7.putEnumerated( idCrop, idcropTo, idboundingBox );
var idPDFG = charIDToTypeID( "PDFG" );
desc6.putObject( idAs, idPDFG, desc7 );
var idnull = charIDToTypeID( "null" );
desc6.putPath( idnull, new File( theFilesTwo[a] ) );
var idFTcs = charIDToTypeID( "FTcs" );
var idQCSt = charIDToTypeID( "QCSt" );
var idQcsa = charIDToTypeID( "Qcsa" );
desc6.putEnumerated( idFTcs, idQCSt, idQcsa );
var idOfst = charIDToTypeID( "Ofst" );
var desc8 = new ActionDescriptor();
var idHrzn = charIDToTypeID( "Hrzn" );
var idRlt = charIDToTypeID( "#Rlt" );
desc8.putUnitDouble( idHrzn, idRlt, 0.000000 );
var idVrtc = charIDToTypeID( "Vrtc" );
var idRlt = charIDToTypeID( "#Rlt" );
desc8.putUnitDouble( idVrtc, idRlt, 0.000000 );
var idOfst = charIDToTypeID( "Ofst" );
desc6.putObject( idOfst, idOfst, desc8 );
var idAntA = charIDToTypeID( "AntA" );
desc6.putBoolean( idAntA, true );
executeAction( idPlc, desc6, DialogModes.NO );
// save the combined files;
theFile.saveAs(new File (theFolderThree + "/file" + bufferNumberWithZeros((a + 1), 4) ), psdOpts)
theFile.close(SaveOptions.DONOTSAVECHANGES)
////// check for psd, tif or jpg //////
function checkFor (theFile) {
if (theFile.name.slice(-4) == ".psd" || theFile.name.slice(-4) == ".tif" || theFile.name.slice(-4) == ".jpg") {return true}
else {return false}
////// buffer number with zeros //////
function bufferNumberWithZeros (number, places) {
var theNumberString = String(number);
for (var o = 0; o < (places - String(number).length); o++) {
theNumberString = String("0" + theNumberString)
return theNumberString

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