The following applications correspond to the bundles folder next to it.  To make that application blank (when adding it to your dock for the theme), copy the bundles folder the application corresponds to and paste it one level up to the folder "/var/stash/theme.xxx/EW Weather@2x.theme/Bundles/".  Then respring.  Note: if there is a parenthesis after the bundle, its because it may contain multiple application's icons

App Store-->com.apple.AppStore
Calculator-->com.apple.calculator
Camera-->
    *4.2.1-->com.apple.camera
    *4.1-->com.apple.mobileslideshow (icon-Camera@2x.png)
Compass-->com.apple.compass
GameCenter-->com.apple.gamecenter
Maps-->com.apple.Maps
Contacts-->com.apple.MobileAddressBook
Calendar-->com.apple.mobilecal
iPod-->com.apple.mobileipod (icon-MediaPlayer@2x.png)
Music-->com.apple.mobileipod (icon-AudioPlayer@2x.png)
Videos-->com.apple.mobileipod (icon-VideoPlayer@2x.png)
Mail-->com.apple.mobilemail
Notes-->com.apple.mobilenotes
Phone-->com.apple.mobilephone
Safari-->com.apple.mobilesafari
Pictures-->com.apple.mobileslideshow (image "icon@2x.png" for 4.2.1.  image "icon-Photos@2x.png" for 4.1)
Messages-->com.apple.MobileSMS
iTunes Store-->com.apple.MobileStore
Clock-->com.apple.mobiletimer
Settings-->com.apple.Preferences
Stocks-->com.apple.stocks
Voice Memos-->com.apple.VoiceMemos
Weather-->com.apple.weather
BiteSMS-->com.bitesms
Overboard-->com.booleanmagic.overboard


For Most other Icons such as appstore icons and icons themed using the Icons folder in Engraved Wood, to make the application blank (when adding it to your dock for the theme), copy the "Sample Blank Icon (for appstore purchase).png" file in this directory.  Then navigate to "/var/stash/theme.xxx/EW Weather@2x.theme/Bundles/" and create a folder called "Icons".  Paste the "Sample Blank Icon (for appstore purchase).png" image into the newly created Icons folder and rename it the EXACT same thing as the application's name on your springboard (capsensitive).  For instance, if the icon you wish to theme is called "SaMpLe 1+2-3" on your springboard, the "Sample Blank Icon (for appstore purchase).png" needs to be renamed "SaMpLe 1+2-3.png" exactly.  Otherwise it will not theme.