Andrew,
The way we've assigned TBM (both versions 1 and 2) is by 'product' by Vendor. An example would be a CDN vendor that offers both file delivery and some value added applications. We would then assign the costs for the 'product' File Delivery to the Tower/Subtower Network/Transport and the apps to Application/Middleware.
We've gone through all of our products from all of our vendors in a similiar fashion, allowing us to have a complete Tower/Subtower view of all costs that we allocate.
We've yet to address the Services layer, but it's on the road map for this calendar year. I'd be interested to hear what you learn about, and to share how this year goes for us as well.
Josh