It's not that you can't have elements on layers other than archicad. But you do need to make sure the elements are on layers that are visible for the drawings on the sheet.
Most times the archicad layer for elements on masters and layouts works as you want.
As a rule of thumb you shouldn't be adding/drawing elements to the layouts.
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"