I am overthinking this. We have an individual who owns several entities, makes cash deposits at the same time for the entities and himself over $10K. We file because funds go between the entities regularly. What dollar amount do we list for him on the CTR, the total or the amount going into his account?

I assume by "because finds go between the entities regularly" you mean you don't consider the entities to be operated independently so you are reporting as if all the deposits are on behalf of the common owner.

If the individual is making all the deposits, you'd have to file whether or not funds move between the entities, and you would include on the Part I entry for the individual the full amount and all the account numbers, but check box 2a only (because you can only check on box in item 2, and it's the first box alphabetically when more than one box could apply). For each of the entities, you'd only include the amount and account number(s) for that entity, and check box 2c.

If you were treating the entities as being operated independently of one another, you would check box 2a for the individual only if a deposit to his account is included. Otherwise you would use box 2b on his section when he deposits to the entities' accounts.