Gilla,
There are many guidelines and definitions so be careful. Best way I've implemented it on a project are (as simply put as possible):
DESIGN PHASE: Make sure the design team is not doing anything too crazy. Spot check system sizing, air exchange rates, building balance, pressurization, specification details, intended controls.
CONSTRUCTION: Inspect frequently. Work with the design engineer's construction administrator on punchlist and communication of punchlist items to the GC. Separately communicate design issues directly to the designer and cc'd to the owner (this is why the design engineer cannot be the CA). The common misconception during this phase is that the CA develops protocols for starting equipment, etc. I've yet to tell a Cleaver Brooks technician how to start up their own boiler and wouldn't recommend you do it. In this phase, work with the subcontractors to ensure duct pressure tests are done and done right; pipe hydros meet spec'd criteria, electrical tests are done, etc.
ACCEPTANCE: Develop test procedures and execute them to prove sequences of operation. Criteria to meet are the SPECIFIED CRITERIA and not the submitted criteria. The specified criteria better meet the design intent. Deviations are documented on commissioning test sheets; some are found to be useful and others cut corners and botch the end result. The controls contractor and balancer account for most basic testing. The CA should find loopholes that COMPLEMENT their work and only repeat it if it is not properly documented. An example is during a cage wash cycle, damper A opens and damper B shuts based on interlock with a Steris washer. If the timing is not right during transition, the exhaust fan trips on low static pressure. Both contractors are done with their jobs, but neither pick up and document this issue that needs correction. Another example is that every zone VAV box closes during unoccupied mode, but the central AHU serving the zones is not specified to shut off, but only go to minimum flow to meet duct static pressure. The AHU in this case is either 1) going to trip on low static pressure or 2) waste energy running when zones do not call for air. Yet another might be the CA's observation of use of chilled water when it's 25°F outside. Such an issue might be related to refining PID controls for economizer dampers and HW and CHW valves.
Be careful that the commissioning requirement does not create another manager in a tie. The commissioning role is to document and improve team execution and building operation, not to try to run around and make sure the air balancer is telling the truth. A bad CA can actually hurt team effort...
Best of luck; construction is a tricky buisness and commissioning is a tricky endeavor. -CB