Well I suppose it depends on what you mean by "manage"
We use CCbill to set up affiliate accounts, keep track of affiliate sales and payout to our affiliates. So far it has been very smooth and efficient. For everything else I search out potential affiliates, communicate with my exisiting affiliates, make and send out promo materials, get or make special request promo materials for affils, all personally. It can get overwhelming to juggle everything! Definitely set up with a processing company that can handle payouts because that helps a lot. I like to be in personal communication with affiliates though. They often know sooo much about advertising and promotions!
Ok so I am starting to ramble but if you want any clarification on what I do with Affils let me know.