Processing a credit card through your payment terminal is always the quickest and safest method of accepting a card payment, but that's not always possible. In the event that you must manually process a card by keying in the number, there are precautionary steps you can take to mitigate the risk of fraud and to prevent chargebacks.
A simple step you can take is to have your customer fill out a credit card authorization form in cases where you do not have an existing relationship with the customer. Doing so will help ensure you have a strong case in the event of any disputes, and will often prevent a dispute from happening in the first place.
You can download the credit card authorization form here.