Alternate fingerings are used for:
Get a good fingering chart for the basic fingerings up to at least high C, if not C# and D. Fingering charts are in many method books. They are also free from many flute and band instrument manufacturers as well as online.
Check out The Woodwind Fingering Guide for a comprehensive online guide to fingerings for all woodwind instruments.
Also important is a good trill chart. The best trill chart in a method book is probably the Rubank Intermediate and Advanced Methods.
The most detailed information about basic fingerings, trills, tremelos and multiphonics available in print is the Pellerite A Modern Guide to Flute Fingerings for the Flute published by Zalo Publications.
Notes with special fingerings to correct pitch
These include open C#, high E, high F#, high G#. See The Woodwind Fingering Guide for a full list.
Examples of using "fake" fingerings to make it easier to play
When you have a lot of high, fast notes to play, using harmonic fingerings can make it much easier. For example, to play high D finger regular G and overblow it, high E finger regular A and overblow, etc. Experiment with these fingerings and consult your flute and/or band teacher about the best times to use these "fake" fingerings.