I am new at this and the owner of the small business I work for sometimes purchases supplies and materials with his own person credit or debit card, and not the business account linked to QuickBooks. He still wants these things to be accounted for in QB... how do I enter them in without messing up the balances? Do I just have to tell him to stop doing it?

Adjust the purchases and have the money paid from the account you need it to come from.

I would reimburse him through your cash account.

Your entry would be to Debit Supplies(or an appropriate account) and Credit Cash.