If you would like to have your icons themed with new Winterboard method (faster), these are the steps.

(For the navigation I used iFile)

1- For Stock and Jailbreak apps, go into root/Applications/appyouwanttotheme.app.
For App Store apps, the way is var/mobile/Applications/randomcode/appyouwanttotheme.app.
There'll be an Info.plist file. Check this line inside it:
<key>CFBundleIdentifier</key>
<string>com.example.example</string>


2- Go to library/themes/yourtheme/Bundles and create a new folder with exactly the same address inside the string. In this case it'll be library/themes/yourtheme/Bundles/com.example.example

3 - Now you just need to drop the desired icon named either icon.png (for most stock apps) or Icon.png. To know which one will work, go into your app folder and look how it's written there.

Please note that you'll maybe have to theme some UIImages for this to show as expected, and they are AppIconOverlay.png and AppIconShadow.png.

Any questions, feel free to ask.