TOWPleasure

I think you have to basically partner with Shopify if you choose them. They take a percentage for their transaction fee. If you only use their merchant processing which is the route most will go, you will have to pay 2.9% plus .30 cents each transaction (depending on the membership level). I know what you're thinking though, one would have to pay a processing fee to a merchant processor either way right? Well, yes but there is a caveat.

See if you have a Shopify site and use their merchant processing plus want to offer PayPal as a payment option, you have to pay an additional percentage over the amount PayPal charges you to Shopify. This could end up adding up much more than one would want once their business starts growing. I have heard good things about Shopify but that aspect of it kills the deal for me. Volusion or Bigcommerce are a better (similar) solution vs Shopify in my honest opinion.