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Here is a comparison of the three tracking methods available in Project Server 2007 and I’m quoting this from the book Microsoft® Office Project Server 2007: The Complete Reference by Dave Gochberg and Rob Stewart.
Percent of Work Complete – This method assumes that the task starts on the scheduled date, and users simply enter a percentage (from 0 to 100) of completed work. Project Server will calculate the actual work based on the percentage complete of planned work.
Actual Work Done and Work Remaining – Regardless of the calendar time, the resource enters overall actual work and remaining work for a task.
Hours of Work Done per Period – Resources are expected to enter their actual work over a given time period. They can enter remaining work on the task to indicate variance from the planned work. This is the preferred option for a best practices approach.
This is important to note because I have experienced a number of fields moving or recalculating as a result of some fields being changed in Microsoft Project. This is frustrating when one does not know what fields automatically recalculate.