Actually I should revise my statement about what lines mark. Mostly because I oversimplified things. Really What the lines mark depends on a number of factors, but most importantly the type of joinery used.

If your tie beams join at the same level as the plate, then perhaps your rafter lines need to mark an edge. If they join above then perhaps the lines need to mark a rafter's center. If below, then it's not really important so long as you are consistent. Or it could be a matter of what you want most to conform to the line. Personally I choose ties and joists because I find interior wall height to be more important. Someone else may choose to set rafters as their standard (which is maybe better in a barn or shed or some such) I will draw up some diagrams to illustrate what I mean.