Batch processing multiple images into one layered file

Well, you can try this script. It will combine two file if the naming is how you state with the files ending in a and b. It will flatten the b file. You can comment out the rasterizing function (ras()) to leave it as a smart object. It will save the file as "c" in the same folder. You will need to change the folder name.

#target photoshop
var srcFolder = new Folder('~/desktop/combine-test/');
var mask = '*a.psd'
var fileList = srcFolder.getFiles (mask);
var psdOptions = new PhotoshopSaveOptions()
psdOptions.layers = true

for(var i=0;i<fileList.length;i++){
    var sndFileName = fileList[i].name.substring (0, fileList[i].name.length-5)
    var sndFile = new File(srcFolder + '/' + sndFileName + 'b.psd')
    var doc = open(fileList[i]);
    placeFile (sndFile);
    ras ();
    doc.saveAs (new File(srcFolder +'/' + sndFileName + 'c.psd'), psdOptions)
    doc.close (SaveOptions.DONOTSAVECHANGES);
    }

    

function placeFile(file){
    var idPlc = charIDToTypeID( "Plc " );
        var desc12 = new ActionDescriptor();
        var idIdnt = charIDToTypeID( "Idnt" );
        desc12.putInteger( idIdnt, 2 );
        var idnull = charIDToTypeID( "null" );
        desc12.putPath( idnull, new File( file ) );
        var idFTcs = charIDToTypeID( "FTcs" );
        var idQCSt = charIDToTypeID( "QCSt" );
        var idQcsa = charIDToTypeID( "Qcsa" );
        desc12.putEnumerated( idFTcs, idQCSt, idQcsa );
        var idOfst = charIDToTypeID( "Ofst" );
            var desc13 = new ActionDescriptor();
            var idHrzn = charIDToTypeID( "Hrzn" );
            var idPxl = charIDToTypeID( "#Pxl" );
            desc13.putUnitDouble( idHrzn, idPxl, 0.000000 );
            var idVrtc = charIDToTypeID( "Vrtc" );
            var idPxl = charIDToTypeID( "#Pxl" );
            desc13.putUnitDouble( idVrtc, idPxl, 0.000000 );
        var idOfst = charIDToTypeID( "Ofst" );
        desc12.putObject( idOfst, idOfst, desc13 );
    executeAction( idPlc, desc12, DialogModes.NO );   
    }

function ras(){
       var idrasterizeLayer = stringIDToTypeID( "rasterizeLayer" );
        var desc16 = new ActionDescriptor();
        var idnull = charIDToTypeID( "null" );
            var ref1 = new ActionReference();
            var idLyr = charIDToTypeID( "Lyr " );
            var idOrdn = charIDToTypeID( "Ordn" );
            var idTrgt = charIDToTypeID( "Trgt" );
            ref1.putEnumerated( idLyr, idOrdn, idTrgt );
        desc16.putReference( idnull, ref1 );
    executeAction( idrasterizeLayer, desc16, DialogModes.NO );
    } 

So what are your specific needs? The easiest, would be to combine all the files and save them as a new file, then you can go back and do whatever editing you need to do.

There have been some other requests like this. You might want to do a search and see if you can fine something that works for you.