I use the deep litter method, but before I would clean out the coop twice a week and even with the deep litter method, I clean the board under where they roost a few times a week.
Not sure about allergies, but I would definitely advise pine shavings. As stated above, cedar isn't good for chickens at all.
If you get the larger pine shavings, they don't have as much dust as the finer shavings, so they shouldn't aggravate your allergies as much.
Pine shavings are more...