How are you managing recurring payments without auto-billing?

How are you managing recurring payments without auto-billing?

I'm a brand new member and read enough to understand there is no support for auto billing. My question is to anyone who works through this, how are you doing it?
 
I charge customers $100 per month and I can set this up through MerchantOne (Not a supported gateway). So I send customers an invoice automatically, then MerchantOne automatically debits their card, then what? I also have Google Checkout but they don't support recurring payments without the API.
 
Do I just tell customers "You'll get invoices but ignore them" and then go in and mark them as PAID manually?
 
There must be a better way. I am not that familiar with invoicing programs and could really use some advice.
 
Thank you.