It's generally just a wrapper around the control panel you are using. They also have different payment gateway options, be it forwarding to 2Checkout, or doing a raw credit card transaction with a merchant gateway like Authorize.Net.
I think he may mean charging customers and collecting payments ?
I have programmed my own system, when the customer pays via PayPal subscription, PayPal will notify me when payments are received, rejected or cancelled, I then update mys system and add cancellations to a list. When customers pay via Cheque or in case i loose an email from PayPal, I will run another admin page (cron job) and it will notify me and the customer of late payments. I can also lookup customers who will pay in the next 7 days.