Basically I run an Ad Network and as we grow the financial aspect is getting more tricky to handle. We started off using Wave App but with no API available it's getting really complicated to use Wave App & Excel.
3 Main Aspects to the business:
- An Invoice is generated each time an Advertiser deposits funds.
- An Invoice is created on behalf of the Developers each time a payout is made.
- Managing Credits. Many Advertisers want to pay on a Net 30 Basis. So something that can help manage this.
Most Startups billed their own, but you could look at Magento (OpenSource), Netsuite (Enterprise) or some kind of Wufoo.com form with Stripe.com integration (Simple).
I'm successfully running a handful of different businesses all using Xero.com as the financial back end.
Two of my businesses (WebReception.com & Searchwords.com) are undertaking the exact tasks you need through the xero saas.
It covers the requirements you've noted above and much more. So consider using it to manage the whole of your business' finances.
It has a good API and a fair handful of apps that are built to work with it.
Zapier.com also offer a bunch of API scripts to communicate with xero.
Let me know if you need any more insight or real world examples.
As per your business, Xero.com or FreshBook would be the best cloud based applications to manage your financials as well as managing receivables efficiently.
With Freshbooks you can integrate payment methods also to give more reasons to your client for motivating them to pay faster, you can also communicate with them through Freshbooks and all your invoice history can be viewable to your clients.