Hi,
I use PTGUI Pro as my Pano stitcher of choice. The Pano stitching quality is superior to that of LR or Photoshop, and it allows much more control in case of difficult projects. I tend to output from Capture One to the default output folder, and move the TIFFs to a specific Pano subfolder. That folder will be where the individual image tiles will be picked up by directing PTGUI to that location, and it can also write its project file there. That produces a simple to manage (and to backup) set of related files.
In case I have to create HDRI's, I first merge the individual tiles into an HDRI, and put those result tiles in another subfolder for stitching.
Cheers,
Bart