There is only one person involved here: John Doe. There are multiple DBA's, but the CTR, unlike the SAR, only facilitates the listing of one DBA name.
When I called the Helpline on this issue I was told to list as many of the DBAs as would fit on the form, separating them with a comma. You may want to make the same call and document the response.
In this world you must be oh so smart or oh so pleasant. Well, for years I was smart. I recommend pleasant.