Lets say you have enabled the Paypal Subscription option in the gateway module so that once client subscribes his invoice from his billing section a subscription ID is created. PayPal sends an IPN to the paypal_return script. So the payment needs to be made from within ModernBill. Subscription Payment, that means a credit was created and if it paid an invoice, you get the subscription number added.
For example : Lets say if a client signs up on 20th and is due on the 1st of every month invoice will be generated before hand as per the settings that you have made in your cron wizard and then subscription will be paid on the 20th of the month. This is the way paypal works. Also you need to be running anniversary billing mode as monthly billing mode does not work properly as this is specific to paypal subscriptions only. Paypal subscriptions work well with Modernbill.
2Checkout doesn’t work all that great, as it is partially manual. 2CO will perform the automatic recurring charge, but it does not report back to modernbill that it has been paid. You need to manually do that yourself.