Ok, you need to SSH into your phone, if you know how to do that, then SSH into your phone to where your themes are. I think its /Library/Themes.
Copy the full .theme folder to your desktop - this makes it a bit easier.
When the full theme is on your desktop, open the folder and you should see a folder called icons, or you may just see a load of icons, each icon represents your app icon. So, Facebook.png is your icon for facebook. Delete the ones you don't want, and drop your new icons in where your old ones were... Your new icons must have EXACTLY the same name as the old one.... so make sure your capitals and spellings are right, and make sure is named "Facebook.png"