I think what the OP is saying is that he uses the Genius Dialer app rather than the standard phone app, but the icon for that app is NOT themed in the theme he is using.
He is asking how he can use the themed icon for the standard phone app to also theme the Genius Dialer app.
OP, to do this you will need to copy some items in the theme around, but first you need to find out what the bundle name is for genius dialer and also what the icon graphic is called (I don't own the app, so can't do this for you).
You can do this in iFile by navigating to the genius dialer application folder (turn on the Application Names setting in iFile to make finding the app folder easier), and find the info.plist file. Within that you will find the details of both the bundle name (something like com.company.appname) and the icon name (probably
[email protected]).
Once you have these details, you need to create a folder within your theme/Bundles folder with the same name as the bundle you just discovered (so the result will be carbonprox.theme/Bundles/com.company.appname or similar).
Then, copy the standard phone app themed icon which will probably be found at carbonprox.theme/Folders/MobilePhone.app/icon@2x~iphone.png to the new bundle folder you just created. I can't tell for sure if this is where the phone icon will be in your theme since I don't have your theme! If the developer used the bundle method it may be elsewhere...
Finally, rename the file to the correct icon name which you discovered at the beginning. If you got everything right, you should be able to respring and the icon will change. If not, check and double check the names. All file and folder names are case sensitive. If you don't get it bang on, it wont work.
Hope that helps, but if you can't get it to work, post the details of the theme and app bundle information that you discover and I'll see if I can clarify the instructions specifically for your situation.