I don't think this is as easy as it sounds. Only two ways to work with spot colors in photoshop: Duotone & adding spot channels to other color modes. So far, so good. Now throw transparency into the mix, and suddenly you have a file that's nearly impossible to import reliably into any application other than Photoshop.
Both Illustrator and InDesign can import PSD files, but only if they're in standard color modes. Anything else, and you'll have to figure out some kind of workaround, like clipping paths, or coloring grayscale images in the layout application. Failing that, you'll have to convert to process.