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If by card faculty you are referring to credit cards (sorry, I'm not familiar with that term), I only used PayPal.
The paypal cart is completely different than zen cart. With the paypal cart you have to build a physical website and incorporate paypal's shopping cart buttons into each page, with zen cart the only thing you need to do is add products to the database and customize it.
Now, if you already have an existing site that is dynamic, it wouldn't be too hard to add the paypal shopping cart. However, if you're dealing with a static website with hundreds of products (or more) - you really should look for another solution (no paypal cart).
For most sellers, paypal takes out 2.9% + .30 per transaction, and you can offset some of these fees (in you sell on ebay) by getting a paypal debit card. If you sell on ebay and use a PayPal debit card, you earn 1% back on purchases when using the debit card as a credit card, plus if you do this you have instant access to your balance any place that you can pay with a credit card.
On one of my ecommerce stores my markup on pricing was very low, I don't have the scripts that I used to calculate my prices, but I think it was around 3%-5% profit on a single item purchase, whether the customer spent $20 or $2000. However, the way to make money on small profit items (from a storefront, not ebay) is to sell multiple items in one transaction and padd the shipping cost a bit - I usually added .50 to shipping costs, and that little bit adds up over time.
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