Georges Gonthier has extensively studied permutations for his proofs of both the 4 color theorem and the Feit-Thompson theorem. His ssreflect package for coq facilitates reasoning about permutations, especially over finite sets, by using computation in Coq rather than using tactics. His seq library is the entry point.
http://ssr2.msr-inria.inria.fr/doc/ssreflect-1.4/Ssreflect.seq.html
You can get the full sources here.
http://research.microsoft.com/en-us/downloads/5464E7B1-BD58-4F7C-BFE1-5D3B32D42E6D/default.aspx
Finally,
http://comments.gmane.org/gmane.science.mathematics.logic.coq.club/4193
discusses 3 representations of permutations.