There are a few different approaches to this; dependant on personal choice and complexity of the project.
Eric Bobrow has a well developed article explaining the merits of each on AECbytes:
http://www.aecbytes.com/tipsandtricks/2008/issue26-archicad.html
You can't turn doors and windows off using layers. In virtual building terms you have to demolish a section of wall containing the door or window and replace it with a new section. You should amend the object ID for the affected element so that you can set up a rule to exclude it from your window schedule.