Of course you need to pass the calls through some piece of equipment which is under your control, and base your billing on the information from it.
Just the “standard” GK (e.g. the one from Cisco) will not be enough (you will not have reliable information about the call start/stop/duration),
you need to setup GK + H323 proxy (or proxying gatekeeper). There are plenty of methods to accomplish this, the best is of course to use the one which is compatible with your billing. If you do not have VoIP billing yet – shop around, there are many of them available, you can choose the one which suites your needs.