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If the corporations are not under the same ownership I would simply file a CTR on XYZ Corp for $13,000 listing the two transactors and check multiple transactions. Lastly, list the account number for XYZ Corp in section #35. There is no need to file one one on ABC if the ownership is different as you only have $3000 being deposited.
The requirement is that you aggregate transactions on behalf of the same party and transactions conducted by the same individual. Since $15,000 was brought in by one conductor, you have to report all of the persons on whose behalf the $15,000 in deposits was made. So you must have TWO Section A entries and, at minimum, one Section B.
The $1,000 cash deposit was made by a second conductor, so it doesn't get aggregated on the basis of a common conductor. If you aggregate the transactions made on behalf of ABC, you get a total of $3,000, so the $1,000 deposit doesn't get reported at all.
Ownership of the two corporations is not relevant unless it's obvious that the only purpose of one of the corporations is to handle funds in ways to avoid CTR filings.