Unless you are known in the industry, and unless you have experience with merchant accounts (in which case you would not be asking this question to begin with ...), I would suggest going with a reliable 3rd party processor such as CCBill or Epoch.
Would-be affiliates will feel much better knowing that their payouts are being handled by a known entity ... and the few points you might save by processing yourself, is certainly not worth the hassles of cutting cheques and everything else involved with processing your own site.
Merchant accounts do not really make sense unless you have a whole network of sites and you are making obscene amounts of $$$ to justify the extra accounting salaries.
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