The Icons from Cydia will not auto skin.  In order to get the skins to work just find the icon you want to use.  I use the cyida icons instead on making my own. Add it to the XboxMB SD theme in it's own folder (i.e com.saurik.Cydia) or whatever the app is called. 

Once the icon is in the corrent folder drag and drop the icon.png file onto the template.  Move the file into the SD Icon folder. You might need to ajust where the icon sits.  Try to get it centered as mouch as possible. Once it looks good just save as a .png over the orginal.  Then just do a respring and the icon should show up.