(I use the Foundations for Superior Performance fingering and trill charts. They're pretty good across the board)
As for understanding - use an alternate fingering when the standard fingering is impractical, impossible, or inconvenient. For example - playing a part on clarinet where you have a third space C followed immediately by a fourth space Eb - use left hand C if you don't have a fancy left-hand-Eb key on your clarinet. You don't want to "slide" unless you have no choice.