Depending how you plan to use your VoIP service, you may not need to know anything about the specific protocols involved in internet-based calling. VoIP protocols are simply the methods and algorithms used during the conversion and transmission of your voice signals. Compatibility across networks is the issue here, especially when multiple users are involved (such as in conference calling).
VoIP providers choose which protocols they use based on the needs of their customers and the equipment they provide. The digital networks of the traditional telecommunications companies (as well as many aspects of the VoIP infrastructure) are based around the H.323 protocol, though the SIP protocol is expected by some to inevitably replace H.323. H.323's place in the telecommunications backbone, however, makes this anything but a sure bet.
Private networks, whether residential or business, use other protocols that VoIP telephony must accommodate. These protocols include PPTP (Point-to-Point Tunneling Protocol), PPPoE (Point-to-Point Protocol over Ethernet), PPPoA (Point-to-Point Protocol over ATM), UDP (User Datagram Protocol), and many others. Some VoIP phones can only be used with certain protocols--but unless you are buying a VoIP phone separately from your VoIP service, you may not need to worry about it.
VoIP protocols are mainly the concern of VoIP service providers, equipment manufacturers, and IT professionals deploying VoIP over large networks. If you will be using your VoIP service over a small business or home network, your service provider should be able to answer your protocol questions quite easily.