Adam:
Speak to your accountant about it.
He (she) might not understand "affiliate" as it relates to online. So you will have to explain it to him in offline terms.
Such as... a salesman who takes the order and money, removes their cut and then passes the rest on to you.
MY take on it... not being an accountant... is that you cannot claim an expense you didn't incur. And this fits that... clickbank takes the money on your behalf, removes their part and then sends you the remaining amount.
With handling your own affiliate payments... it does become an expense because you get all the money and then spend some of it. Just like processing a credit card with your merchant account - you get the money and then later the credit card fee is taken out of your account.
Remember... I am NOT an accountant and this is NOT accounting advice. For proper accountig advice see an account - and for legal advice see a lawyer.
Michael Ross
For businesses see here