New Post: How do I turn payment methods/gateways on and off?

Have a look in the checkout module settings for some gateway options.

To only have the cheque/manual gateway visible, uncheck the PayPal one.

To get rid of the default text that displays above the card gateways - Clear out the Back Office gatewaymsg.text template.

If you are using the default templates and no card gateways at all, then you might see a border around the empty box where the card gateway graphic was. You can put this into the Back Office stylesheetoverride.css template to hide that:

.CardGatewayButton, .ManualGatewayButton{border:1px solid #FFFFFF;}

That assumes your skin has a white background.
Rob