I use Quickbooks as well.
I tried all kinds of different billing/payment solutions for my hosting clients and in the end I just put them all in Quickbooks. I run each of our online stores through Quickbooks so all my customers/clients are in one central place.

Set it up using the memorize transactions feature - you can select that the invoices are created X number of days before the payment is due. Then use the bulk email feature to send out the invoices so everyone is aware. On the due date process their payment from the CC information you have on file for them.

If you look after it everyday or every other day it works well.

Like I said, I've tried all kinds of software but the Quickbooks solution worked best for me.