Some folks cube their stitched image. Then take the 6 sided image into photoshop where the zenith (ceiling) and nadir (floor) are a cubed flat face. Then in photoshop they bring in their company logo on a single layer and position it over the hole. In photoshop you would then flatten the logo layer onto the background.
Of course then you would have to convert the cubed image back into a spherical. In the past this has caused issue with cubed seam edges appearing as white and blue line in the spherical image.
OR.. why not just use Panoweavers ADD FLOOR AND CEILING options using your own 200 x 200 caps. In photoshop make a transparent background circle 230 x 230 or 200 x 200 what ever dimension covers your tripod legs in the final panorama. Some trial test for transparent circle size should provide some good results.
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EasyPano - Panoweaver