While your bike is away in storage, you don't need to have a battery inside of it. The main important thing when winterizing your bike in regards to its battery is that you need to keep it indoors, warm and dry. You should not leave your bike battery outside in the cold, as doing this will freeze your bike battery. When a battery freezes, the solution expands, and then when you go to start it up in the warmer months, your battery will be cracked and spill the acid all over your bike! This, in case you have not yet figured it out, is very, very bad.
If you happen to have a place to store your bike where it won't be exposed to freezing temperatures, then it's perfectly okay to leave the battery in your bike.
You will want to keep your battery charged, however, no matter where you store it. It is important to either put your bike on a "Smart Charger", or a "Trickle Charger". You should continually charge your bike battery throughout the winter. You do not want to "over-charge" your battery, just keep it charged periodically throughout the winter.
You will also need to check the fluids on your battery on a regular basis to ensure that those fluids are not boiling, and clean the battery on a regular basis following manufacturers instructions. If acid has leaked outside of the battery, usually the manufacturers will give you instructions to clean it with baking soda and water. If your battery is maintenance free, do not let the name fool you. You will still need to clean the terminals; instructions should be on the battery information from the manufacturer.
