To make life a bit easier, before you start with any complicated stuff - may I recommend you take a look at either "ThemeIconMaker" (free) or IconHarvester ($4.99).
What both of these tweaks do is use your theme's icon masks to automatically create a themed icon for you. Then, when you activate the theme (in Winterboard), the icon you want is themed.
I like IconHarvester for the reason you mentioned - it seems to grab the icons better than TIM does. Plus, it gives you the option of deciding which icon to use (the theme's design or stock). For example, here is a shot of me customizing a theme. See how I have the option to pick icons for BytaFont, Calculator, Calendar and Camera:
Essentially, if the masks exist in the theme (AppIconMask, AppIconOverlay, AppIconOverlay), i've not yet had IconHarvester create a themed icon (to include the stock or Cydia icons that are normally so hard to theme).
I can't speak so much about TIM as I don't use it - but I know that you don't get the option to select which icon to use with TIM...
This is just a suggestion - but speaking as someone who is a compulsive themer (and theme tinkerer

), I think this might work for you. Maybe it's a thought?
Marilyn