Our online presence won't come for awhile but we will use a custom built CMS that uses a database and flexible 'front-end' integration system to allow us to do what we do best on our own site. Billing we will use a credit card processor something like WorldPay, PayPal and 2Checkout just don't cut it.
Project management will be with the CMS. We have developers all over the place and this makes it easier if they can get online and see what needs to be done next and by when. Client management will be the same, custom built boards, support systems, new project etc.
I don't want to go into much detail because simply, it's ours