I have a question about checking box 34 on the CTR for deposit/withdrawal. Am I correct that if our customer cashes checks not from his checking account that I would not check this box. He is not withdrawing from an account here only cashing a check. Also if they cash two checks than I would check multiple transaction right?

You would (IMO) check negotiable instrument cashed, and yes if there's more than one you would check multiple transactions.