Merge two Mat-Objects in OpenCV

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I wrote a little function in order to be able to "stick" the pixels of an image on top of another, but it somehow doesnt work: While the "shapes" of my "sticked" image is right, the colors are not.

The example flower is the first image, and as a second image I had a black trapezoid png. As you can see, there are multiple problems: 1. The colors are shown weirdly. Actually there are no colors, just greyscale, and some weird stripes as overlay. 2. Alpha values are not respected. The white part of the overlay image is transparent in the png.

Here is my code:

void mergeMats(Mat mat1, Mat mat2, int x, int y){
    //unsigned char * pixelPtr = (unsigned char *)mat2.data;
    //unsigned char * pixelPtr2 = (unsigned char *)mat1.data;
    //int cn = mat2.channels();
    //int cn2 = mat2.channels();
    //Scalar_<unsigned char> bgrPixel;

    for (int i = 0; i < mat2.cols; i++){
        for (int j = 0; j < mat2.rows; j++){
            if (x + i < mat1.cols && y + j < mat1.rows){

                Vec3b &intensity = mat1.at<Vec3b>(j+y, i+x);
                Vec3b intensity2 = mat2.at<Vec3b>(j, i);
                for (int k = 0; k < mat1.channels(); k++) {
                    intensity.val[k] = saturate_cast<uchar>(intensity2.val[k]);
                }
                //pixelPtr2[(i + x)*mat1.cols*cn2 + (j + y)*cn2 + 0] = pixelPtr[(i + x)*mat2.cols*cn + (j + y)*cn + 0];
                //pixelPtr2[(i + x)*mat1.cols*cn2 + (j + y)*cn2 + 1] = pixelPtr[(i + x)*mat2.cols*cn + (j + y)*cn + 1];
                //pixelPtr2[(i + x)*mat1.cols*cn2 + (j + y)*cn2 + 2] = pixelPtr[(i + x)*mat2.cols*cn + (j + y)*cn + 2];
            }
        }
    }
}

The commented code was another approach, but had the same results. So, here are my questions:

1. How do I solve the 2 problems (1. the colors..., 2. alpha ...)

2. How is the pixel-array of any Mat-Object actually, well, organized? I guess it would be easier for me to manipulate those arrays if I knew whats in them.

(I already asked this question on stackoverflow, but I guess it's better to ask it here.)