How do you guys keep track of all your income and expenses? It would be easier if all income and expenses went through your bank account but with Paxum and Paypal as intermediaries it becomes a little confusing.
For example, some traffic sources I pay with my credit card and wire transfer and others with Paypal and Paxum. Some affiliate networks pay me through wire transfers, Paypal or Paxum.
Anyone have a specific system for this?
Muchas Gracias 
We use Clearbooks in the UK, but our accountant handles most of it by hand, exporting and importing PDFs/CSVs from online bank statements etc.
Xero.com + Accountant / Bookeeper
Quickbooks syncs with PayPal. You can also add your credit cards.