Hello all,
The way I do it is a bit of a pain in the doodah but works.
First hide all the layers in the main image so all you have visible are the images you wish to merge together.
Then flatten the image.
Open another paint window.
Then copy the flattened image and paste it to the new window.
Then click undo to unflatten the main image.
Then remove all the flattened and copied images from this main image.
Then copy the flatten image and paste it to your main image.
With any luck the flattened image will go into the right place on the main image.
Kev