You can collect payments any way you want, and still use vCita for invoicing.
You can decide you only accept checks, or swipe the credit card when the client visit your office, or over the phone.
You can also offer your clients the choice of paying online when they receive the invoice, or pay you with an alternative payment method.
Either way, once you received a payment from your client, you can mark the invoice as paid.
To learn more on how to create and manage invoices click here