First, thank you for the question. Second, all that I can see attached to your post is the same print example uploaded twice, once as "Example-1" and again as "Example-2."
Based on your description, I may be able to imagine the arrangement in which the carried numbers appear.
In response to your questions:
1) I would include the whole spatial multiplication arrangement in Nemeth mode. That is, I would put the open Nemeth Code indicator before the column headings and the Nemeth termination indicator after the end of the arrangement. This means that you canNOT use contractions in the column headings. Perhaps a key is in order?
2) I would suggest that you use the carried number indicator in the way that best represents the print layout. If this means that you place carried numbers above the indicator where they appear that way in print and below the carried number indicator where they appear that way in print, then so be it. You should include a TN explaining the multiple placements of carried numbers.
Many kudos to you for sticking with this job that has proven to be more than you anticipated. The braille reader will benefit from your dedicated and thoughtful work.