Business A account deposits for $10,000 cash total
Business B account deposits for $10,000 cash total
Transactor 1 brings in $20,000 cash plus $100 change order (currency exchange)

I am filing a CTR because the transactor brought in over $10,000 cash and I report on both businesses.
Do I leave both businesses at $10,000 and report the cash for Transactor 1 as $20,100?
Do I split the $100 change order between the two business? Do I just pick a business and attribute the $100 to one of their totals?

Any opinions on how to approach?

The appropriate method would have been to ask on whose behalf the currency exchange was conducted. From there, you will have your answer.

The person bringing in the money definitely is $20,100. Beyond that, your guess is as good as mine. Your best option is to train your tellers to ask on which business' behalf the change order was conducted. Without that information, you are left guessing where to put the $100.

As I was typing, I thought that same thing. Makes perfect sense.
Thank you both for your help