If you're using a program like bettercut or folder organizer, you can keep them on your sdcard and use one of those programs to create shortcuts with your new icons. This will only replace the icon for the app on your homescreen.
If you want to replace an icon from an application completely (in app tray and anywhere else it shows up), you have to pull the .apk file and replace the icon(s) in it, then push it back. This only works with applications in the /system/app/ directory, so you will need root access to do this. I'd recommend searching for a how-to guide for modifying .apks. There are several out there that explain it much better than I could.
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