Okay there are 2.. no wait let's say 3 ways to bomb.
If the precision bombsite is enabled, the green "+" is where your bombs will hit. Your bombsite is already calibrated.
If you have autocalibrate enabled (it was put in a while back, to help alleviate problems with the old bomber calibration system) you have to go to the bombsite and look at the instructions on the top left of the screen. Hit "u" to enter the calibration screen. It says you must hold down "y" for at least 2 seconds. I have done some tests, and what it does is it oscilates back and forth past your current speed, and finally the oscillations get smaller until it is at your current speed. Holding "y" for 2 seconds will most likely have you calibrate your speed on one of the oscillations, meaning your speed and the calibrated speed will be wrong (thus bombs fall wrong). HOLD FOR AT LEAST A COUNT OF 15!!! That's the secret. I've found that by counting til 15 seconds you usually get reliable speed. Hit "u" to get back to drop mode, drop bombs. Note your bomber must be steady. Don't calibrate just after levelling out, or you'll accelerate past that calibration speed (say you calibrate right after auto level, you will calibrate at about 160 or so, but by the time you get to target you could be going 250). YOu need time and distance to make your speed steady. Check E6B.
If you do NOT have autocalibrate enabled, it's harder (for my computer, and some others', it is impossible, it just won't happen). You go to bombsite. You hit "u" to ener calibration mode. Open your clipboard. Select the target on the map and click on it (the altitude will be set in the top left side of your screen). Close clipboard. Move your crosshairs UP (forward) and find some landmark. Hold the crosshairs on that landmark and hold the "y" key down. Keep the crosshairs steady on the landmark (whatever it is) for as long as you can. Keep the crosshairs steady as you can. Then let go of "y" and hit "u". You should be calibrated. Note that you must also be at steady speeds here. Holding the crosshairs on some landmark and holding the "y" key down is how you measure your speed in this method of calibration.
How do you tell what mode you have?
If you have a green "+" you don't have to calibrate.
If you enter calibrate mode and the text on your top left screen only shows certain things in red, only do those things (hold down Y to calibrate speed, etc) -- generally if you don't have to click the clipboard, you have autocalibrate and you just need to set your speed.
If all items on the calibration screen are red, do them all!