I've just upgraded from 'Receipts in a Shoebox v2.1' to Quickbooks Regular 2006

I have an accountant but just want to keep better track of my money. Then I realised how different affiliate marketing works to a "normal" business. I mean, I don't create invoices and send them to companies.. I'm an affiliate, they just mail me a cheque when it's due.
Also, paypal. I do loads of crap with paypal - little payments in and out to random people and companies. Don't really track it very well and just record the "withdrawn amount" I put into my bank.
So two questions, do you make invoices and then close them as paid when you receive your cheques (even though you never mail the company an invoice)?
And, do you track individual payments in and out using paypal or just put the amount you withdrawn into quickbooks, again, as a paid invoice?
Agghhh now I know why I have an accountant, and I'd call him except he's on fucking holday
