The whole reason why I want to register at mybitcoin is that I'm under the impression that you MUST go this route in order to accept BTC payments for a web-store, but maybe I'm wrong, if somebody has experience using different means, would appreciate a note on that. I'm setting that up for OpenCart based store.
I don't know anything about OpenCart, but you don't need mybitcoin.com (or similar) to accept payments on a website.
It's possible to install and run bitcoin directly on your server, however it's a bit more complicated.