If you can issue API calls from your programming environment, you can use GetModuleFileName(0, buffer, lengthof(buffer)) to get the full pathname of your EXE file. Then you strip out the filename component, and you have the path-we're-running-from. Alternatively if you're coding in C/C++, you can use argv instead of the API call.
Then, when you need to access a file, you have to concatenate the running-from path with the filename, instead of hardcoding absolute paths.
Also, if you want to play cleanly with non-administrative user accounts (required to work properly under Vista!), you should use the %APPDATA% environment variable instead of running-from path.