Over, always. The pant leg goes on the outside of the tall rubber boot so that rain, snow and splash run away from the boot opening. Tuck them in and you funnel water straight down onto your socks, which is exactly the thing you're trying to prevent.
This is why the ankle opening matters when you're buying. Fitted softshells, narrow ski pants and fashion rain pants often won't clear a tall expedition boot. When ordering online, check the ankle measurement and the return policy rather than going on waist size alone.
Try them with a similar tall boot before you travel. Sit, step up onto a chair, squat, walk up stairs. The pants shouldn't pull tight at the knee or ride up above the boot top when you bend.