For a CTR you need to describe two types of persons -- In section A you must provide the name(s) of the person(s) on whose behalf the transaction is conducted (use of the words "beneficiary" and "benefactor" is inaccurate and the cause of lots of misunderstandings on who gets reported on a CTR). And in Section B, you describe the individual or individuals who conducted the transactions.
I read your question to say that Doe is buying the checks on behalf of the Mouses (or is that "Mice"?
). That is, the Mouses asked him to purchase the checks for them. In that case, Mickey Mouse would be in one Section A entry and Minnie Mouse in a second Section A entry, with John Doe in Section B.
On the other hand, if your question should be read to say that Mickey and Minnie Mouse are the payees on the checks and that John Doe is buying the checks to pay Mickey and Minnie Mouse from his own funds (he owes them money or wants to give them the money), then John Doe conducted the purchase on his own behalf, and John Doe only goes in Section A, with Section B completed with a single check of the "conducted on own behalf" box.
If I have misread your question, please clarify for me.