You can manually process any pending deposits through the
Transaction->Pending Deposits menu. These are transactions, which are either still waiting for the member to submit payment through a third party payment processor (eg. PayPal, 2CheckOut), or credit card charges that have only been authorized, and still need to be captured (fully charged).
The page contains one section, which looks something like:

The table lists all pending deposits currently in your database. For deposits made through a third party payment processor there is also a Pay Now link, which you can click on to be automatically redirected to the payment server. To process deposits, check all transactions you would like to process, then complete the few questions, and click on the Process Transaction submit button.
The first question asks for the status of the transaction, and can either be approved or declined. The second question asks whether or not you would like to process the transaction(s) though your merchant account. This is only applicable if you are using a real merchant account (eg. AuthorizeNet, VeriSign, Moneris Solutions). If yes, the software will automatically send a request to the merchant account behind the scenes, to capture the credit card authorization.
The third question asks if you would like to send e-mail notifications or not. If yes, the software will check the existing notifications you created through the Communicate->Notification Settings menu, for any matching the transaction, and send out the appropriate e-mail messages. The last question allows you to specify an additional note, which will be displayed when someone views details of the transaction.