Here are the steps:
1. Set the payment module in Authorize Only or Auth Only mode.
2. When a customer places an order the payment will be authorized but, not captured.
3. To capture the payment login into the Magento admin area and click on the order you want to capture.
4. Click on the "Invoice" button on the top right.
5. Check the invoice and right bottom you will find a drop down with the option "capture online".
6. Select "Capture Online" and then, submit. This will capture the order payment.
Please note, once you capture the full amount you will not see the 'Capture Online' option.