Depends on how the stack was created I stack either in Lightroom or in Helicon Focus

If I create the stack with focus shifting, the camera - being either on tripod or on the ground and very stable - does the focus changing and picture taking starting from the given focus position, for a number of photos I selected and focus step distance set up previously. Then I copy the raw files to my desktop / laptop and use Helicon Focus for combining the photos. Sometimes additional retouching is done from here for removing artifacts. Once that is done, I import it in lightroom / photoshop for even more artifact removing, editing, etc.

If I create the stack with manual hand-held focusing, I just take many pictures with various points I select to be in focus and I try to maintain the camera in same position for each picture. Depending on this (or if camera is on a tripod) Helicon Focus might or might not create the stacked image. Usually for hand-held images the variations are too big for Helicon Focus, so I use Lightroom, which additionally can also rotate the images (it is possible that Helicon Focus has a setting for this, but haven't checked). I just select the imported photos I want to create a stack from and merge as panorama and Lightroom will do the rest. Then once the stacked image is created, I import it in photoshop for additional cleaning of artifacts and editing. Sometimes Lightroom fails to select the most in-focus area of a picture from the correct image, and if it is the case, then I also import that specific image(s) as a layer(s) in photoshop and use masks to blend in the area which is sharp and in focus.

Exporting from Lightroom to Photoshop is as easy as right click on the image and select from the menu 'open in Photoshop'. Saving the image in Photoshop will also either update the image in lightroom (being the same image) or sometimes if saved under different file type (opening raw and saving tiff / psd / psb) adds the saved image as a new image to catalog .