One timeline per project. Noah is describing how you can create the Motion equivalent of AE’s nesting comps by nesting layers, but if you want multiple versions of the same animation/composite, then you have to create multiple layers and toggle them enabled/disabled as needed. If you want separate versions, you have to save separate files.
Have you tried using the PROVIDE FEEDBACK menu item under the MOTION application menu?
Jim Kanter,
Digital Film Institute
http://www.dfilminst.com