Preparing your lotus for winter can mean different things in different parts of the country. In warmer winter climates, lotus can winter in place. You should allow your lotus leaves to wither and turn brown, once they have turned brown you may cut the stems above the water line. That's basically all you have to do until your lotus begin to send out new leaves in the spring.
In colder climates, allow your lotus leaves to wither and turn brown. Once this has occurred, you may cut the leaves and stems slightly above the water line. If the lotus are growing in pots in shallow water, you can lower the pots to an area below the frost/freeze line and move them back up in the spring.
If your lotus are growing in a bog area, allow the leaves and stems to wither and turn brown before cutting them back. You can mulch the lotus with fallen leaves that you have bagged as long as you are able to uncover them for growth in the spring.
You can allow your lotus plants to wither and turn brown outdoors and them bring them indoors and store them in a cool environment until the tubers have used all of the energy in the leaves and stems. Once the leaves and stems are entirely spent, you can cut off the leaves and stems and keep the tubers in a dark,cool environment until spring. This way you can be assured that the tubers have absorbed all of the energy possible from the stems and leaves--maximizing the amount of growth energy and sustenance available.
I live in Ohio, I allow my lotus to wither and turn brown each fall before cutting them above the water line. My lotus are exposed to several frosts and freezes but the tubers themselves never freeze as they are in pots with 4-6 inches of water over the top of the pots.
In the spring, I turn the pots over and sort out the dead or dying tubers, these ones are usually dark brown or black and feel soft. I place the newer tubers back in the pots and add soil and water. As soon as the daylight cycles and warmer temperatures arrive, the tubers are off and running again!
I hope I have impressed upon you the importance of allowing your lotus leaves and stems to wither and turn brown. Even though I love a tidy water garden, allowing the leaves and stems to wither--allows your lotus to absorb as much energy as possible and to become a much stronger plant the following year.
If planted correctly, your lotus should grow and bloom the very first year!