MA standard is as you explain. You hit U to uncage the sight, then hold Y for a few seconds to set the speed. Compare calibrated speed to ground speed and if they match, you're set.
Manual mode, typically used in FSO and AvA needs a couple of extra steps. After U to uncage the site, you need to bring up the map and hold the left-shift key and then click the target on the map to set the target's altitude. Then while holding the Y key, you use your joystick to keep the bombsite crosshairs steady on a ground feature to set your ground speed. If all goes well, your E6B ground speed will match your calibrated speed. If not, repeat until close and tweak your speed with throttle and/or rpm to get a match.