Because transient variations in atmospheric conditions can cause unpredictable variations in the atmospheric extinction it is necessary to regularly monitor the standard stars throughout a night's observing. When making photometric observations care and caution pay dividends. A typical strategy might be to start the night's observing with a series of observations of standard stars, covering a range of zenith distances. These observations can be used to make a preliminary estimate of the atmospheric extinction. Then as the night progresses observations of standards are regularly interspersed amongst the observations of programme objects.
Often modern observatories will have software which allows approximate `rough and ready' reductions to be carried out in near real time, thus allowing instrumental magnitudes to be computed for the standard stars pari passu the continuing observations. This facility is extremely useful because it allows the atmospheric extinction to be monitored as the night progresses. However, reductions carried out during the observing session are only approximate. They are useful for monitoring the atmospheric extinction, but are not the most accurate results obtainable from the observations.
You should always reduce your data after the observing session has finished, starting from the full set of observations.
Passing clouds and light mist will obviously affect the atmospheric extinction. Furthermore, they can be difficult to detect by eye, even if you regularly look outside the telescope dome (it is difficult to see light cloud at night with eyes that are not dark-adapted). However, it is easy to spot any deterioration in the observing conditions if the atmospheric extinction is being monitored regularly. Observations of programme objects can be suspended until good conditions return. Using these techniques, and with good conditions and modern instrumentation, it is perfectly feasible to carry out photometry to an accuracy of 0.01 magnitude without resorting to any special tricks.
It is prudent to keep a note of the Right Ascension, Declination and UT or sidereal time of each observation (for both standard stars and programme objects) as it is made. Usually (though not always) the air mass or zenith distance will be calculated automatically and added to the header information for each observation as it is written. However, if you have kept your own notes you can calculate these quantities yourself if necessary, either as a check or because they are not otherwise available. (See Appendixfor further details of calculating the zenith distance.)
The CCD Photometric Calibration Cookbook