If I am understanding you correctly, the business acount is owned by Some Company, and the DBA account is owned by Doe, and perhaps another individual. If that's the case, then deposits to the two account are not aggregated for a common beneficiary.
HOWEVER, if you identify that the deposits have a conductor in common, and that individual conducts more than $10k in currency, then you do have cause for a CTR, and will report all affected accounts accordingly.