How merchant sites work?

Please tell me how merchant sites like ebay and others work in detail. Also tell me how the online payment sites work. Also tell me which is the best payment site?

Better you ask one question at a time, and clarify what you want to ask.

OK first tell me how the payment sites work?

I think you want to know about the process of online payment. If you want to add online payment facility in your website, you need to have a payment gateway on your website through which you can accept credit cards in your website. There are two ways to add this facility on your website either you should have a merchant account or sub merchant account. Opening a merchant account is very expensive and need paper works and third party validation, need ssl, verisign or thawte certification etc. there are many other thing which I do not know.
For smaller sites there is facility of sub merchant account you can use payment gateway of third party like ccavenue or abcpaymentgateway or 2checkout etc.
Opening submerchant account is not very costly, you can setup this under Rs. 10,000/-

I would like to know something like this. Suppose I order a digicam from ebay or from any other online store. while paying I give my credit card info. Then why will they not charge more than the amount mentioned as the price? Is it only because that their business will slow down? Or is their any option where i will be able to mention the amount to be deducted? Please dont take this question as an annoying one or a stupid one as i really want to have a clear idea before proceeding any further. Thanks!

why will they not charge more than the amount mentioned as the price?

Why should they charge more. Customer can claim chargeback, if his credit card is overcharged.

Or is their any option where i will be able to mention the amount to be deducted?

Generally what amount to be charged is passed programatically to payment processor, therfore there is no option for buyer to mention the amount