This might become necessary if you want to add content to an already existing PDF file, e.g. when doing pre-press work for flyers etc.. For example, you might resize one PDF file to have additional place on the page, and put other content into that free space.
Get yourself two PDF files to overlay on each other, both of the same page size (else automatic resizing is employed), and both one-sided.
Then use this command to generate the combined PDF file with overlays:
pdftk file1.pdf background file2.pdf output out.pdf