I don not use APP, I use PTGui. However, I would imagine that APP has the ability to create a template from a stitch (PTGui does this). The basic idea is to use, for example, your 0EV series to create your stitch. This image set will determine how the images are distorted and transformed to create the final stitch. The idea is to apply this master set of transforms identically to each pano sequence - ensuring that you are creating the exact same stitch for each exposure value across the HDR sequence. Once the template is created from the successful 0EV stitch, you can apply the template to each of the other exposure sets, getting the exact same stitch each time. Then, you will end up with a set of 16bit TIFFs, for example, that are full panoramas at each of your exposure values. You can then import these panos into PM and combine them, with the assurance that they are identical in size and image registration. This, of course, assumes that you used a tripod and that each exposure for a particular pano segment is registered with its mates at that pano segment.
So, my workflow when I do this in PTGui:
1) Use smallish JPEGs of my 0EV exposures - I shoot RAW with a Canon 15mm full-frame fisheye with a 5D classic which permits me to shoot 6 around, 1 zenith and 3 nadir shots (to remove the tripod) for a full spherical 360°wide x 180° tall equirectangular pano.
2) I complete the stitch of my 0EV small JPEGs so that I get the image warp and transformations aligned, using some manual control points to straighten verticals, etc. This is now the Master stitch - I save all of these transformations as template in PTGui. I use small JPEGs so that this initial stitch is more responsive to adjustments and previews of the stitch as I work. It does not matter, as the transforms applied to the small JPEGs are the same as those required for the full-res RAWs.
3) I then bring each full-res exposure sequence of RAWs into PTGui and apply the template to it. PTGui spits out a stitch that is identical in transform to the template - I do this for each exposure value. Sometimes I might convert the RAWs into linear TIFFs prior to stitching, if I feel I need more control over the RAW conversion process than the automatic stuff PTGui does (say I need to correct WB prior to stitching).
4) Now I have output 16bit TIFFs of each pano stitch, at each exposure value in my sequence. I can combine them into a single HDR or exposure blend in any app I want. Because I applied a stitch template, each stitch is identical - as long as there is not any significant shifting of the camera between exposures for a specific pano segment, the HDR combination should need no alignment. The issue one may run into at this point is the sheer size and memory requirements for a merge that involves 3 or 5 or 7 images that each may be 12,000 by 6,000 pixels, for example. I do not use Photomatix, so this type of HDR combination might be an issue should you choose this workflow. As an alternative, consider a free app like Picturenaut - I believe it is capable of combining large images - I think the authors have done gigapixel HDR panos with it. You can then save the resulting dataset as HDR, EXR, etc. and tonemap it wherever you chose.
PTGui will do all of this with the image set (ie, create a full HDR pano) but stitching each exposure with a template gives me more flexibility to perform the HDR merge or exposure blend outside of PTGui.
Good luck!
Kirk
