predcon: there's some problems it doesn't cover ... through Control Panel, it seems to think that the two secondary L and R triggers are the Z-Axis, and that the D-pad is a Hat Switch, and that the right analog stick is the X and Y Rotation.
This is by design, and works exactly the same with a real 360 controller.
The triggers are an axis to provide analog sensitivity for throttle-style input in games that support that (even many older games recognise them for this purpose, mostly racing/simulation-style games). Because the assignments fit legacy expectations older games will usually see all of the controls, although some may have problems with the triggers depending on how they supported joystick throttle axes back in the day (some see them as a single button, others don't see them at all) and some may see only one or neither of the right analog axes for the same reason. These are technical limitations of the games themselves, not your particular controller.
Xpadder doesn't require you to map all controls at once, so one possibility is to use the game's own controller support for all inputs it sees and then use Xpadder for the remaining ones it can't see.
EDIT: these detection problems only apply to older games, of course; new games designed with 360 controllers in mind will see everything, and since Windows itself sees your controller as a real 360 controller you shouldn't have any problems. All Valve games and most Games for Windows games fully support 360 controllers and will make a note of this on the box/store entry/etc.