Husband is S - corp ... not sure he's been doing things correctly

Linda,
My husband set up his S corp in August of this year. Some of the payments for services were made out to him personally, and the company's bank wouldn't accept them for deposit. Instead of asking for these companies to redo the check, he just deposited them in our personal account. He isn't trying to hide the money, and is claiming all of these checks as income. We have an appt. next week with the accountant, but I'm trying to find out what kind of trouble, if any, he could get in to.
I've now taken over all the bookkeeping, because the financial aspect of the business isn't his strong suit.