When you want to charge a client for a service that is not included in a point of sale product or his membership, you can create an extra invoice manually.
When you go to the client's profile, click on the tab "invoices". Here, above the list of all his existing invoices, will be a button to create a new one. Just fill in the information required and create the invoice. After this, you can treat it as any other invoice, you can choose a payment method and even use the invoice in your next SEPA batch.
If you want to create an invoice manually because you need to charge a person that is not (yet) your client and therefore not in the system, you can do this by going to the financial app. In the tab "invoices" you can click on "create new invoice" and fill in the details. Make sure that the box with "guest?" next to it, is ticked.