MATLAB Compiler finds all *.m, *.p, MEX-files, etc. that your application calls, and packages them into a CTF Archive. It then generates a C/C++ wrapper that calls into your main .m file. So, your .p file is actually part of the CTF archive that is packaged with your executable. I don't think there is a reliable way to simply re-generate a new .p file and somehow plug it into the deployed application. As far as I know, you will need to re-compile the application if the .p changes.
Typically .mat files are added to the CTF archive when you add them under the "Additional Files" section in DEPLOYTOOL or use the -a option with the MCC command (I'm not sure if MATLAB Compiler automatically grabs it, but intuition says that it doesn't). You can probably use UIGETFILE to ask the user to specify a .mat file, so that a new one can be specified each time. Or, you could store the MAT-file at a common location on all deployment machines, and always look at that path.
