nerd619,
Are you using the Pad Editor in ak.Sys? Each sample has to be added to a program, whether you dial it in or drag and drop. You choose the pad mapping that way.
RobV,
Each sound is a sample that is assigned to a pad. A collection of samples makes up a program. There are two types of programs, Drum and Key group. Most of the time you will create Drum programs. The MPC4000 also uses something called a "Multi". Programs get assigned to Multis. Read the User Guide for basic operations.