William,
Because automatic connector lines and regular lines are not designed to go together necessarily, that may explain some of the issue. That said, try the following:
1) Click the round SmartDraw Menu Button in the upper left of the screen and choose "Options > Allow Lines to Link".
2) Right-click on the org chart line linking the shapes currently and select "Lock Object".
3) Using the Shape Connector Line or the straight line tool from the Home tab (whichever meets you needs best) draw the lines you need between the necessary shapes. Then apply the necessary formatting (line style, etc.)
Note: I would advise you to do this line creation last as the lines will not move with the rest of the automatic connector lines if something gets adjusted.
See if that helps at all.
Regards,
SmartDraw Support