What kind of framework are you running on the site now? Depending on what you have gives you different options varying in difficulty. If you answer a few questions and I should be able to help out better.
1. If you are active in the bitcoin community, would you like to have everything done yourself? This includes just accepting bitcoins and either spending them or converting them to fiat on your own through an exchange. This is obviously going to be the cheapest option but also the most work.
2. If you have a supported framework you can always look into a company such as BitPay which can do each part of the processes for you if you would like. They have a number of extensions available:
https://bitpay.com/bitcoin-shopping-cart-plugins The downside of this is you will be paying extra fees to the company you use.
Simply accepting payments on a site yourself you need to keep track of a few more things then going through a secondary company. You will need to (ideally) have a number of bitcoin addresses pre-generated in a database where you can pull one address for each payment. Then you have to make sure each address is only used once, the address is only used for that transaction and who/what transaction that payment is for. Keeping track of this stuff isn't that difficult and you can use a combination of other services like
http://www.bitping.net/ to let you know when you receive payment or manually/api call to
https://blockexplorer.com/ to verify payment was sent.
Easiest steps for accepting payment yourself:
1. Create table in a database with bitcoin receive addresses and expired field
2. When at checkout, pull one address from database and set it expired
3. Add receive address to transaction/order
4. Verify payment (manual/api/etc)
