The mortises and pegs will follow - the Rubies only require you to draw the male joinery. The mortises do not need to be drawn on the timbers show they will automatically show up when you cut a section and they are imported and cut when you use the Rubies.
In my workflow I do not do any joinery* until the final phase before the frame enters the shop. I have my library of timbers drawn with a boxed 'x' in the ends - this way when I cut a section @ the face of a timber I see the boxed 'x'. I detail the frame as needed to client presentation - and after the frame goes through the approval process I do the joinery. At this time it is unlikely that things will move - as you are getting ready to cut the frame.
When I have a moment I'll post and example of my section slice method.
*sometimes I'll use a brace or a floor joist with the joinery attached - but I tend to keep things simple until the wood is on its way to the shop - and this comes from years of working with AutoCAD HSB and translating my workflow to SketchUp.
