The most complete description of the physics going into DarkSUSY is
P. Gondolo, J. Edsjö, P. Ullio, L. Bergström, M. Schelke and E.A. Baltz, JCAP 0407 (2004) 008 [astro-ph/0406204].
Please refer to this if you use DarkSUSY. Please also remember to cite the original work, which you use from DarkSUSY.
Included in the download of the source are also the test programs dsmain.f, dstest.f and dstest-isasugra.f that shows how to use DarkSUSY.
You can also look at the manual either in pdf format (or a short version without routine headers: Manual-short.pdf).
You can also take a look at the talk describing DarkSUSY 5.0 given at Tools 2008.