How can I cover a wood stove pipe where it passes through the second floor?
Sounds like the flue pipe runs through your room. This pipe should definitely be insulated, not only for comfort, but for safety as well. Insulating the pipe keeps the heat in the pipe, preventing the buildup of creosote, which is a fire hazard.

You will need to wrap that pipe with high-temperature insulation made specifically for that purpose. Do not use anything not specifically rated and designed for insulating metal chimney liners. However, this may not be a DIY job. Combustion appliances and ventilation are serious business. You may want to hire a pro.