I was wondering the same thing. I posted a question on tripadvisor yesterday and here is the answer I received from Darkbeer:
The original plan was to have the Monorails closed for about a year and a half, but it got changed, mainly due to the request of the hotels.
What will happen is that starting the Tuesday (subject to change), instead of doing a "full loop", the Monorails will switch to shuttle service, and only offer one way trips. Basically the Monorails will load at either Tomorrowland or Downtown Disney (the hotel stop) and then go thru Disney's California Adventure to the other station. It will then unload, and go in the oppisite direction to the original station.
This way, they avoid going over the old Submarine Lagoon, which will allow for the construction for the new Finding Nemo ride.
The shuttle service will go from Janaury thru Labor Day.
After Labor Day, the Monorail will shut down until mid-2007. This will allow for remodeling of the Tomorrowland Station, and the new queue for Finding Nemo, which will be right below the station.
Hope that helps a bit,
Kathy