one thing you have to make sure is to get the bundle correctly identified.
As an example. If I wanted to change the icon for the Twitter App, i need to find out what the ID is of the app and what the icon name is.
So using the AppInfo app, find the Twitter app and click on it. It will bring up a window showing things like version, folder, etc.
What you need to make note of is the ID and the IconFiles name.
For Twitter, the id would be com.atebits.Tweetie2
the IconFile name would most likely be
iconproduction@2x.png
Now, using iFile, go into the theme bundles you want to add the icon to. In this case, we'll stick with the Glasklart theme:
var/stash/Themes.xxxxx (you'll see some extension letters after theme)/Glasklart Icons.theme
then select Bundles
Once in Bundles, select "edit" in top right and then click on the + sign at the bottom left.
Create your own bundle (it's just a directory name) using the EXACT ID of the icon you want to create, in our example it was Twitter.. so create a folder called: com.atebits.Tweetie2
Once this has been created copy your icon into this folder and rename it
iconproduction@2x.png
That's all there is to it.
Just remember that you need to create the bundle using the EXACT ID listed for the app that you found using AppInfo.
Hope this helps.