What I would do, and some people may disagree with my philosophy, is take any related segments and put them in timelines together.
For menus, I would do one menu for each timeline, having a button for each segment in that timeline. Then set the end action of each chapter to go back to the menu. (Do not put an end action if it is the last chapter of a timeline, simply put the end action on the timeline)
For a play all effect, if you choose to go that way, create Chapter Playlists for each of the timelines and link those in a way that suits your fancy in a regular playlist.