Here's what I'd do (and there are many ways to do this I'm sure)

Use Camera Raw or Lightroom to generate 16bit tiff images of your pano segments.

In PS go to file/scripts/load files into stack - in that dialog select 'attempt to auto align', see what happens.

If things line up nicely you select your pano layers and use edit/autoblend and you're pretty much done, unless you have to touch up stuff before autoblend and maybe transform for perspective, etc. You could use a duplicate set for the above step too, if you want to maintain your original images. Save original pano work file as PSD or PSB, flatten and downsample to 8bit for distribution.

AFA "use the Photomerge tool on raw images", I don't believe you can do 'anything' with raw images - you need to convert them into something first, like tif, jpg, psd whatever.

good luck!

I've just recently been using my new GigaPan Epic Pro and their Stitch software - it works very nice w/raw images too, but will export only flattened files.

Does the Kolor Autopano Pro product retain layer integrity on export?

I do panoramas in Photoshop CS5 and now CS6 starting with the RAW files.  I work on RAW files from Bridge and after I complete the RAW adjustments in ACR, I click the Done button and it saves the settings and returns me to Bridge.  If you want to have 16 bit files, set  ACR to 16 Bits with the color profile you want (16 bits with sRGB, aRBG, or Pro Photo RGB) before you click the Done Button.  In Bridge, select the RAW files you want to use in the Panorama and then click "Tools > Photoshop > Photomerge.  This will switch to Photoshop with Photomerge active and the RAW files selected.  Make and anjustments you want in the Photomerge box and the click the OK button.  Photomerge will open the RAW files in 16 bit mode using the profile you selected and generate a Panorama.  After it completes I click on the Megre Visible, rotate the image if required,  and then select the visible image do an invert selection and grow the selection by 5 pixels and run "Content Aware Fill" if required.  Then flaten the image, crop, and save as required (16 bit TIF it that's what you want).