"Stacking" images means something differently in Aperture. Aperture has stacks, but a stack of images is a set of image versions collapsed and hidden behind a single thumbnail, to make browsing and tagging easier.
What you want to do is image compositing, and that is something that Aperture does not support at all. Aperture provides no tools to combine elements from different images into one single image or to layer images. I'd recommend to use Adobe Photoshop or elements, pixelmator, or the free Gimp as an external editor to do compositing.
Here's what I do for focus-stacking, HRD, and other multiple-exposures-to-one-final-image processes. Modify to suit .
- Import files into Aperture.
- Stack them.
- Assign a color label I don't use for anything else (this alerts me to what they are, and keeps me from mistakenly using or deleting them).
- White balance and any other adjustments that should be done at this point (un-correct the exposure, if I forgot to lock it in the field).
- Select all and export to a Finder folder (I have folders already in place for panoramas.
- Use another program to combine the exported files and create the new one.
- Import the new one into the same Project in Aperture.
- Drag it into the Stack (the Aperture Stack -- what Léonie mentioned), and make it the Stack Pick. Collapse the Stack.
- Delete all the files in the Finder folder.
- Prepare the new Image for publication.
It's more roundabout than one might want, but it works well (imho).