Even though it has been mentioned some people seem to still not ralize that there are no cups on a 2008 Madone. That's the beauty. It also isn't proprietary either. It uses standard "off-the-shelf" cartridge bearings.
The problem comes from the fact that most of the Trek dealers have no idea what bearing sizes are used.
Sorry to state the obvious here, but I assume you had bearings on the original Bonty crank right? Those bearings will (most likely) work for a DA crank as well. Why do you want to swap them? They are not attached to the crank.