The key to successfully calibrating is to push your joystick forward in the F6 view after toggling the U key. This swivels the bombsight forward so you can select a terrain feature you will use to calibrate with. Zoom (Z key then ] key) in on any feature (terrain tile intersection, bldg, etc.) and hold the crosshair over the feature by applying back pressure on the stick, then press and hold the Y key to "start the clock."
Continue using back pressure on your stick to keep the crosshair over the feature as you count off 5-10 seconds. Don't be too concerned if the crosshair floats away from the feature, but make sure it is back over it when you release the Y key.
Bring up the map on the clipboard and zoom in using the Insert key. Shift + click with mouse on the target to set Target Altitude. Don't be sloppy about this part. If your target is a town, make sure you click on the map room (yellow square) and not just somewhere near the airfield. The town may be a different altitude than the airfield.
Press the U key again to toggle out of calibration mode.
You only have to set the Target Altitude one time and may recalibrate without setting it again.
Once you understand the concept on pushing the bombsight forward with your stick and holding the crosshair over a feature, you should be just as accurate bombing with this method as with the simplified bombsight method. Good luck!