Just copy them somewhere to the side, they will be gone once you turned the end result into the morph.
Personally I find 'drag a copy' faster than copy+paste.
Since the meshes will be gone, the layers don't really matter.
Generally a template will have a layer that is invisible in most layer combinations for keeping elements that are temporary and such.
Before diving in head first, I would recommend getting a few days of basic ArchiCAD training from an experienced tutor. You will be mucking about for many months by trying to find out things by yourself. At the very least follow the 4 or 5 training series that Graphisoft has available on Youtube.
Erwin Edel, Project Lead, Leloup Architecten
www.leloup.nlArchiCAD 9-26NED FULL
Windows 10 Pro
Adobe Design Premium CS5