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You use the Layers module - it's fairly intuitive, and incredibly powerful.
The way to fix different image sizes is to load them both up in Nebulosity and align them, saving each individual file. Neb is great in that it allows the user to load up different-dimensioned files. I think DSS has a more accurate alignment procedure overall, but it demands identical dimensions. So I use both - getting the file dim right in Neb, then doing the re-alignment in DSS. A little fiddly perhaps, but minor in the grander scheme of things and it really helps, whether you're aiming at HDR combining or simply RGB channels.
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