Server 2003 file and dir. permissions.

I have obtained a server at work with Microsoft Windows 2003 Server Enterprise Edition as the operating system but seem to be having problems setting up shares correctly. I am utilizing this server running a financial application that’s maintained on an Air Force base where my employment currently is. I want to copy the application files from my older NT 4.0 server to the new one and share it so base member can access to run the program. I would appreciate any assistance in the matter.