As far as I know, you use Customize or Summerboard to change apps' icons, carrier logos, battery icons, etc. But, you would either have to install themes (through Installer) or upload your own icons through an interface such as ibrickr, iPhonebrowser, etc.
So if you have your own set of .png files that you want to use, you would have to upload them, either directly into the firmware or into the appropriate folders in either Customize or Summerboard.
Ok, what you are trying to do requires SSH installed on your iPhone and WinSCP (if you are on Windows) or Fugu (if you are on the Mac).
Once you have the icon you want it must be named icon.png and placed in the /Applications/AppName.app/ folder. It will overwrite the existing icon.png. You replace AppName.app with the name of the application. The only exceptions to this are photo and camera are named something different and so is iPod. I can't remember what they are off the top of my head, but look in their directories and you'll see them.