As Karl F. says, model everything at the correct elevation. Use the Reference Levels to set up to 3 elevation values. Each time you place any element, you are given a choice of which reference level you are placeing it relative to. e.g. the chair on the active story or the dock relative to the sea.
1. Set your Project reference levels: Options> Project Preferences> Reference Levels
2. Choose to which reference level you are placing each object relative.
Erika
Architect, Consultant
MacBook Pro Retina, 15-inch Yosemite 2.8 GHz Intel Core i7 16 GB 1600 MHz DDR3
Mac OSX 10.11.1
AC5-18
Onuma System
"Implementing Successful Building Information Modeling"